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comparison maaslin-4450aa4ecc84/src/lib/SummarizeMaaslin.R @ 1:a87d5a5f2776

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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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0:e0b5980139d9 1:a87d5a5f2776
1 #####################################################################################
2 #Copyright (C) <2012>
3 #
4 #Permission is hereby granted, free of charge, to any person obtaining a copy of
5 #this software and associated documentation files (the "Software"), to deal in the
6 #Software without restriction, including without limitation the rights to use, copy,
7 #modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
8 #and to permit persons to whom the Software is furnished to do so, subject to
9 #the following conditions:
10 #
11 #The above copyright notice and this permission notice shall be included in all copies
12 #or substantial portions of the Software.
13 #
14 #THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
15 #INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
16 #PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
17 #HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
18 #OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
19 #SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
20 #
21 # This file is a component of the MaAsLin (Multivariate Associations Using Linear Models),
22 # authored by the Huttenhower lab at the Harvard School of Public Health
23 # (contact Timothy Tickle, ttickle@hsph.harvard.edu).
24 #####################################################################################
25
26 inlinedocs <- function(
27 ##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
28 ##description<< Creates a summary of association detail files.
29 ) { return( pArgs ) }
30
31 #Logging class
32 suppressMessages(library(logging, warn.conflicts=FALSE, quietly=TRUE, verbose=FALSE))
33
34 # Get logger
35 c_logrMaaslin <- getLogger( "maaslin" )
36
37 funcSummarizeDirectory = function(
38 ### Summarizes the massline detail files into one file based on significance.
39 astrOutputDirectory,
40 ### The output directory to find the MaAsLin results.
41 strBaseName,
42 ### The prefix string used in maaslin to start the detail files.
43 astrSummaryFileName,
44 ### The summary file's name, should be a path not a file name
45 astrKeyword,
46 ### The column name of the data to check significance before adding a detail to the summary
47 afSignificanceLevel
48 ### The value of significance the data must be at or below to be included in the summary (0.0 is most significant; like p-values)
49 ){
50 #Store significant data elements
51 dfSignificantData = NULL
52
53 #Get detail files in output directory
54 astrlsDetailFiles = list.files(astrOutputDirectory, pattern=paste(strBaseName,"-","[[:print:]]*",c_sDetailFileSuffix,sep=""), full.names=TRUE)
55 logdebug(format(astrlsDetailFiles),c_logrMaaslin)
56
57 #For each file after the first file
58 for(astrFile in astrlsDetailFiles)
59 {
60 #Read in data and reduce to significance
61 dfDetails = read.table(astrFile, header=TRUE, sep=c_cTableDelimiter)
62 dfDetails = dfDetails[which(dfDetails[astrKeyword] <= afSignificanceLevel),]
63
64 #Combine with other data if it exists
65 if(is.null(dfSignificantData))
66 {
67 dfSignificantData = dfDetails
68 } else {
69 dfSignificantData = rbind(dfSignificantData,dfDetails)
70 }
71 }
72
73 #Write data to file
74 unlink(astrSummaryFileName)
75 if(is.null(dfSignificantData))
76 {
77 funcWrite("No significant data found.",astrSummaryFileName)
78 return( NULL )
79 } else {
80 #Sort by metadata and then significance
81 dfSignificantData = dfSignificantData[order(dfSignificantData$Value, dfSignificantData$P.value, decreasing = FALSE),]
82 funcWriteTable( dfSignificantData, astrSummaryFileName, fAppend = FALSE )
83 # Sort by q.value and return
84 return( dfSignificantData[ order( dfSignificantData$P.value, decreasing = FALSE ), ] )
85 }
86 }