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Uploaded the version running on the prod server

author	george-weingart
date	Sun, 08 Feb 2015 23:08:38 -0500
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1 a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	1 MaAsLin User Guide v3.1
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	2 =======================
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	3
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	4 September 2013 - Updated April 2014 for Galaxy
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	6 Timothy Tickle and Curtis Huttenhower
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	7
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	8 Table of Contents
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	9 -----------------
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	10
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	11 A. Introduction to MaAsLin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	12 B. Related Projects and Scripts
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	13 C. Installing MaAsLin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	14 D. MaAsLin Inputs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	15 E. Process Flow Overview
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	16 D. Process Flow Detail
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	17 G. Expected Output Files
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	18 H. Troubleshooting
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	19 I. Installation as an Automated Pipeline
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	20 J. Commandline Options (Modifying Process and Figures)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	21
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	22 # A. Introduction to MaAsLin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	23
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	24 MaAsLin is a multivariate statistical framework that finds
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	25 associations between clinical metadata and potentially
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	26 high-dimensional experimental data. MaAsLin performs boosted additive
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	27 general linear models between one group of data (metadata/the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	28 predictors) and another group (in our case relative taxonomic
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	29 abundances/the response). In our context we use it to discover
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	30 associations between clinical metadata and microbial community
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	31 relative abundance or function; however, it is applicable to other
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	32 data types.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	33
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	34 Metagenomic data are sparse, and boosting is used to select metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	35 that show some potential to be useful in a linear model between the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	36 metadata and abundances. In the context of metadata and community
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	37 abundance, a sample's metadata is boosted for one Operational
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	38 Taxonomic Unit (OTU) (Yi). The metadata that are selected by boosting
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	39 are then used in a general linear model, with each combination of
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	40 metadata (as predictors) and OTU abundance (as response
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	41 variables). This occurs for every OTU and metadata combination. Given
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	42 we work with proportional data, the Yi (abundances) are
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	43 `arcsin(sqrt(Yi))` transformed. A final formula is as follows:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	44
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	45 ![](https://bitbucket.org/biobakery/maaslin/downloads/maaslinformula2.png)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	46
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	47 For more information about maaslin please visit
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	48 [http://huttenhower.sph.harvard.edu/maaslin](http://huttenhower.sph.harvard.edu/maaslin).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	49
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	50
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	51 # B. Related Projects and Scripts
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	52
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	53 Other projects exist at www.bitbucket.com that may help in your
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	54 analysis:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	55
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	56 * QiimeToMaAsLin is a project that reformats abundance files from
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	57 Qiime for MaAsLin. Several formats of Qiime consensus lineages are
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	58 supported for this project. To download please visit
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	59 [https://bitbucket.org/timothyltickle/qiimetomaaslin](https://bitbucket.org/timothyltickle/qiimetomaaslin).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	60
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	61 * merge_metadata.py is a script included in the MaAsLin project to
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	62 generically merge a metadata file with a table of microbial (or
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	63 other) measurements. This script is located in `maaslin/src` and
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	64 is documented in `maaslin/doc/ Merge_Metadata_Read_Me.txt`.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	65
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	66
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	67 # C. Installing MaAsLin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	68
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	69 R Libraries: Several libraries need to be installed in R these are
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	70 the following:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	71
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	72 * agricolae, gam, gamlss, gbm, glmnet, inlinedocs, logging, MASS, nlme, optparse, outliers, penalized, pscl, robustbase, testhat, vegan
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	73
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	74 You can install them by typing R in a terminal and using the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	75 install.packages command:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	76
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	77 install.packages(c('agricolae', 'gam', 'gamlss', 'gbm', 'glmnet', 'inlinedocs', 'logging', 'MASS', 'nlme', 'optparse', 'outliers', 'penalized', 'pscl', 'robustbase', 'testthat'))
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	78
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	79 # D. MaAsLin Inputs
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	80
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	81 There are 3 input files for each project, the "\.read.config" file, the "\.pcl" file, and the "\.R" script. (If using the sfle automated pipeline, the "\" in the file names can be anything but need to be identical for all three files. All three files need to be in the `../sfle/input/maasalin/input` folder only if using sfle). Details of each file follow:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	82
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	83 ### 1\. "\*.pcl"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	84
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	85 Required input file. A PCL file is the file that contains all the data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	86 and metadata. This file is formatted so that metadata/data (otus or
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	87 bugs) are rows and samples are columns. All metadata rows should come
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	88 first before any abundance data. The file should be a tab delimited
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	89 text file with the extension ".pcl".
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	90
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	91 ### 2\. "\*.read.config"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	92
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	93 Required input file. A read config file allows one to indicate what data is read from a PCL file without having to change the pcl file or change code. This means one can have a pcl file which is a superset of metadata and abundances which includes data you are not interested in for the run. This file is a text file with ".read.config" as an extension. This file is later described in detail in section F. Process Flow Overview subsection 4. Create your read.config file.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	94
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	95 ### 3\. "\*.R"
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	96
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	97 Optional input file. The R script file is using a call back programming pattern that allows one to add/modify specific code to customize analysis without touching the main MaAsLin engine. A generic R script is provided "maaslin_demo2.R" and can be renamed and used for any study. The R script can be modified to add quality control or formatting of data, add ecological measurements, or other changes to the underlying data before MaAsLin runs on it. This file is not required to run MaAsLin.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	98
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	99 # E. Process Flow Overview
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	100
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	101 1. Obtain your abundance or relative function table.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	102 2. Obtain your metadata.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	103 3. Format and combine your abundance table and metadata as a pcl file for MaAsLin.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	104 4. Create your read.config file.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	105 5. Create your R script or use the default.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	106 6. Place .pcl, .read.config, .R files in `../sfle/input/maaslin/input/` (sfle only)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	107 7. Run
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	108 8. Discover amazing associations in your results!
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	109
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	110 # F. Process Flow Detail
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	111
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	112 ### 1\. Obtain your abundance or relative function table.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	113
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	114 Abundance tables are normally derived from sequence data using
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	115 Mothur, Qiime, HUMAnN, or MetaPhlAn. Please refer to their documentation
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	116 for further details.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	117
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	118 ### 2\. Obtain your metadata.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	119
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	120 Metadata would be information about the samples in the study. For
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	121 instance, one may analyze a case / control study. In this study, you
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	122 may have a disease and healthy group (disease state), the sex of the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	123 patents (patient demographics), medication use (chemical treatment),
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	124 smoking (patient lifestyle) or other types of data. All aforementioned
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	125 data would be study metadata. This section can have any type of data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	126 (factor, ordered factor, continuous, integer, or logical
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	127 variables). If a particular data is missing for a sample for a
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	128 metadata please write NA. It is preferable to write NA so that, when
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	129 looking at the data, it is understood the metadata is missing and it's
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	130 absence is intentional and not a mistake. Often investigators are
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	131 interested in genetic measurements that may also be placed in the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	132 metadata section to associate to bugs.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	133
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	134 If you are not wanting to manually add metadata to your abundance
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	135 table, you may be interested in associated tools or scripts to help
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	136 combine your abundance table and metadata to create your pcl
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	137 file. Both require a specific format for your metadata file. Please
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	138 see the documentation for QiimeToMaaslin or merge_metadata.py (for
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	139 more details see section B).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	140
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	141 ### 3\. Format and combine your abundance table and metadata as a pcl
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	142 file for MaAsLin.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	143
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	144 Please note two tools have been developed to help you! If you are
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	145 working from a Qiime OTU output and have a metadata text file try using
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	146 QiimeToMaaslin found at bitbucket. If you have a tab delimited file
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	147 which matches the below .pcl description (for instance MetaPhlAn
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	148 output) use the merge_metadata.py script provided in this project
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	149 (`maaslin/src/merge_metadata.py`) and documented in
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	150 `maaslin/doc/Merge_Metadata_Read_Me.txt`.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	151
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	152 ###PCL format description:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	153
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	154 i. Row 1 is expected to be sample IDs beginning the first column with a feature name to identify the row, for example "ID".
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	155
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	156 ii. Rows of metadata. Each row is one metadata, the first column entry
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	157 being the name of the metadata and each following column being the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	158 metadata value for that each sample.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	159
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	160 iii. Row of taxa/otu abundance. Each row is one taxa/otu, the first
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	161 column entry being the name of the taxa/otu followed by abundances of
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	162 the taxa/otu per sample.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	163
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	164 iv. Abundances should be normalized by dividing each abundance measurement by the sum of the column (sample) abundances.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	165
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	166 v. Here is an example of the contents of an extremely small pcl file;
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	167 another example can be found in this project at
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	168 `maaslin/input/maaslin_demo.pcl`.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	169
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	170
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	171 ID Sample1 Sample2 Sample3 Sample4
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	172 metadata1 True True False False
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	173 metadata2 1.23 2.34 3.22 3.44
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	174 metadata3 Male Female Male Female
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	175 taxa1 0.022 0.014 0.333 0.125
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	176 taxa2 0.406 0.029 0.166 0.300
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	177 taxa3 0.571 0.955 0.500 0.575
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	178
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	179
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	180 ### 4\. Create your read.config file.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	181
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	182 A *.read.config file is a structured text file used to indicate which
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	183 data in a *.pcl file should be read into MaAsLin and used for
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	184 analysis. This allows one to keep their *.pcl file intact while
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	185 varying analysis. Hopefully, this avoids errors that may be introduced
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	186 while manipulating the pcl files.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	187
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	188 Here is an example of the contents of a *.read.config file.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	189
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	190 Matrix: Metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	191 Read_PCL_Columns: Sample2-Sample15
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	192 Read_PCL_Rows: Age-Height,Weight,Sex,Cohort-Profession
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	193
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	194 Matrix: Abundance
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	195 Read_PCL_Columns: Sample2-Sample15
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	196 Read_PCL_Rows: Bacteria-Bug100
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	197
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	198 The minimal requirement for a MaAsLin .read.config file is as
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	199 follows. The Matrix: should be specified. Metadata needs to be named
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	200 "Metadata" for the metadata section and "Abundance" for the abundance
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	201 section. “Read\_PCL\_Rows:” is used to indicate which rows are data or
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	202 metadata to be analyzed. Rows can be identified by their metadata/data
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	203 id. Separate ids by commas. If there is a consecutive group of
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	204 metadata/data a range of rows can be defined by indicating the first
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	205 and last id separated by a “-“. If the beginning or ending id is
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	206 missing surrounding an “–“, the rows are read from the beginning or to
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	207 the end of the pcl file, respectively.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	208
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	209 A minimal example is shown here:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	210
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	211 Matrix: Metadata
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	212 Read\_PCL\_Rows: -Weight
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	213
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	214 Matrix: Abundance
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	215 Read_PCL_Rows: Bacteria-
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	216
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	217 With this minimal example, the delimiter of the file is assumed to be
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	218 a tab, all columns are read (since they are not indicated
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	219 here). Metadata are read as all rows from the beginning of the pcl
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	220 file (skipping the first Sample ID row) to Weight; all data are read
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	221 as all rows from Bacteria to the end of the pcl file. This example
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	222 refers to the default input files given in the MaAsLin download as
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	223 maaslin_demo2.\*.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	224
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	225 ### 5\. Optionally, create your R script.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	226
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	227 The R script is used to add code that manipulates your data before
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	228 analysis, and for manipulating the multifactoral analysis figure. A
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	229 default “*.R” script is available with the default MaAsLin project at
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	230 maaslin/input/maaslin_demo2.R. This is an expert option and should
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	231 only be used by someone very comfortable with the R language.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	232
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	233 ###6. Optional step if using the sfle analysis pipeline. Place .pcl, .read.config, and optional .R files in `../sfle/input/maasalin/input`
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	234
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	235 ###7. Run.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	236
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	237 By running the commandline script:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	238 On the commandline call the Maaslin.R script. Please refer to the help (-h, --help) for command line options. If running from commandline, the PCL file will need to be transposed. A script is included in Maaslin for your convenience (src/transpose.py). The following example will have such a call included. An example call from the Maaslin folder for the demo data could be as follows.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	239
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	240 ./src/transpose.py < input/maaslin_demo2.pcl > maaslin_demo2.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	241 ./src/Maaslin.R -i input/maaslin_demo2.read.config demo.text maaslin_demo2.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	242
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	243 When using sfle:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	244 Go to ../sfle and type the following: scons output/maaslin
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	245
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	246 ###8. Discover amazing associations in your results!
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	247
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	248
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	249 #G. Expected Output Files
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	250
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	251 The following files will be generated per MaAsLin run. In the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	252 following listing the term projectname refers to what you named your "\*.pcl" file without the extension.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	253
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	254 ###Output files that are always created:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	255
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	256 projectname_log.txt
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	257
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	258 This file contains the detail for the statistical engine. This can be
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	259 useful for detailed troubleshooting.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	260
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	261 projectname-metadata.txt
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	262
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	263 Each metadata will have a file of associations. Any associations
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	264 indicated to be performed after initial variable selection (boosting)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	265 is recorded here. Included are the information from the final general
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	266 linear model (performed after the boosting) and the FDR corrected
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	267 p-value (q-value). Can be opened as a text file or spreadsheet.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	268
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	269 projectname-metadata.pdf
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	270
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	271 Any association that had a q-value less than or equal to the given
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	272 significance threshold will be plotted here (default is 0.25; can be
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	273 changed using the commandline argument -d). If this file does not
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	274 exist, the projectname-metadata.txt should not have an entry that is
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	275 less than or equal to the threshold. Factor data is plotted as
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	276 knotched box plots; continuous data is plotted as a scatter plot with
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	277 a line of best fit. Two plots are given for MaAslin Methodology; the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	278 left being a raw data plot, the right being a corresponding partial
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	279 residual plot.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	280
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	281 projectname.pdf
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	282
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	283 Contains the biplot visualization. This visualization is presented as a build and can be affected by modifications in the R.script or by using commandline.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	284
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	285 projectname.txt
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	286
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	287 A collection of all entries in the projectname-metadata.pdf. Can be
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	288 opened as a text file or spreadsheet.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	289
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	290 ###Additional troubleshooting files when the commandline:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	291
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	292 data.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	293
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	294 The data matrix that was read in (transposed). Useful for making sure
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	295 the correct data was read in.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	296
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	297 data.read.config
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	298
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	299 Can be used to read in the data.tsv.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	300
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	301 metadata.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	302
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	303 The metadata that was read in (transposed). Useful for making sure the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	304 correct metadata was read in.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	305
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	306 metadata.read.config
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	307
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	308 Can be used to read in the data.tsv.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	309
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	310 read_merged.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	311
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	312 The data and metadata merged (transposed). Useful for making sure the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	313 merging occurred correctly.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	314
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	315 read_merged.read.config
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	316
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	317 Can be used to read in the read_merged.tsv.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	318
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	319 read_cleaned.tsv
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	320
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	321 The data read in, merged, and then cleaned. After this process the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	322 data is written to this file for reference if needed.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	323
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	324 read_cleaned.read.config
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	325
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	326 Can be used to read in read_cleaned.tsv.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	327
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	328 ProcessQC.txt
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	329
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	330 Contains quality control for the MaAsLin analysis. This includes
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	331 information on the magnitude of outlier removal.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	332
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	333 Run_Parameters.txt
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	334 Contains an account of all the options used when running MaAsLin so the exact methodology can be recreated if needed.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	335
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	336 #H. Other Analysis Flows
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	337
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	338 ###1. All verses All
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	339 The all verses all analysis flow is a way of manipulating how metadata are used. In this method there is a group of metadata that are always evaluated, as well there are a group that are added to this one at a time. To give a more concrete example: You may have metadata cage, diet, and treatment. You may always want to have the association of abundance evaluated controlling for cage but otherwise looking at the metadata one at a time. In this way the cage metadata is the \D2forced\D3 part of the evaluation while the others are not forced and evaluated in serial. The appropriate commandline to indicate this follows (placed in your args file if using sfle, otherwise added in the commandline call):
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	340
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	341 > -a -F cage
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	342
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	343 -a indicates all verses all is being used, -F indicates which metadata are forced (multiple metadata can be given comma delimited as shown here -F metadata1,metadata2,metadata3). This does not bypass the feature selection method so the metadata that are not forced are subject to feature selection and may be removed before coming to the evaluation. If you want all the metadata that are not forced to be evaluated in serial you will need to turn off feature selection and will have a final combined commandline as seen here:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	344
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	345 > -a -F cage -s none
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	346
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	347 #I. Troubleshooting
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	348
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	349 ###1\. (Only valid if using Sfle) ImportError: No module named sfle
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	350
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	351 When using the command "scons output/maaslin/..." to run my projects I
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	352 get the message:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	353
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	354 ImportError: No module named sfle:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	355 File "/home/user/sfle/SConstruct", line 2:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	356 import sfle
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	357
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	358 Solution: You need to update your path. On a linux or MacOS terminal
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	359 in the sfle directory type the following.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	360
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	361 export PATH=/usr/local/bin:`pwd`/src:$PATH
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	362 export PYTHONPATH=$PATH
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	363
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	364
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	365 ###2\. When trying to run a script I am told I do not have permission
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	366 even though file permissions have been set for myself.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	367
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	368 Solution: Most likely, you need to set the main MaAsLin script
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	369 (Maaslin.R) to executable.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	370
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	371 #J. Installation as an Automated Pipeline
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	372
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	373 SflE (pronounced souffle), is a framework for automation and
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	374 parallelization on a multiprocessor machine. MaAsLin has been
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	375 developed to be compatible with this framework. More information can
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	376 be found at
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	377 [http://huttenhower.sph.harvard.edu/sfle](http://huttenhower.sph.harvard.edu/sfle). If
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	378 interested in installing MaAsLin in a SflE environment. After
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	379 installing SflE, download or move the complete maaslin directory into
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	380 `sfle/input`. After setting up, one places all maaslin input files in
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	381 `sfle/input/maaslin/input`. To run the automated pipeline and analyze
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	382 all files in the `sfle/input/maaslin/input` directory, type: `scons output/maaslin`
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	383 in a terminal in the sfle directory. This will produce
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	384 output in the `sfle/output/maaslin` directory.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	385
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	386 #K. Commandline Options (Modifying Process and Figures)
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	387
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	388 Although we recommend the use of default options, commandline
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	389 arguments exist to modify both MaAsLin methodology and figures. To see
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	390 an up-to-date listing of argument usage, in a terminal in the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	391 `maaslin/src` directory type `./Maaslin.R -h`.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	392
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	393 An additional input file (the args file) can be used to apply
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	394 commandline arguments to a MaAsLin run. This is useful when using
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	395 MaAsLin as an automated pipeline (using SflE) and is a way to document
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	396 what commandline are used for different projects. The args file should
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	397 be named the same as the *.pcl file except using the extension .args
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	398 . This file should be placed in the `maaslin/input` directory with the
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	399 other matching project input files. In this file please have one line
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	400 of arguments and values (if needed; some arguments are logical flags
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	401 and do not require a value), each separated by a space. The contents
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	402 of this file will be directly added to the commandline call for
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	403 Maaslin.R. An example of the contents of an args file is given here.
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	404
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	405 Example.args:
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	406
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	407 -v DEBUG -d 0.1 -b 5
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	408
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	409 In this example MaAsLin is modified to produce verbose output for
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	410 debugging (-v DEBUG), to change the threshold for making pdfs to a
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	411 q-value equal to or less than 0.1 (-d 0.1), and to plot
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	412 5 data (bug) features in the biplot (-b 5).
a87d5a5f2776 Uploaded the version running on the prod server george-weingart parents: diff changeset	413

Mercurial > repos > george-weingart > maaslin

annotate maaslin-4450aa4ecc84/README.md @ 1:a87d5a5f2776