annotate test-data/fpkmSCV.txt @ 4:ba8fde59843d draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit 00a7926c285bc4a339bd7deebf40b28f39c7d947-dirty
author devteam
date Tue, 21 Jul 2015 14:18:39 -0400
parents 587c425b4e76
children 78fcfc04fcfe
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
1
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
3 Copyright (C) 2014 The R Foundation for Statistical Computing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
4 Platform: x86_64-unknown-linux-gnu (64-bit)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
5
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
6 R is free software and comes with ABSOLUTELY NO WARRANTY.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
7 You are welcome to redistribute it under certain conditions.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
8 Type 'license()' or 'licence()' for distribution details.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
9
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
10 Natural language support but running in an English locale
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
11
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
12 R is a collaborative project with many contributors.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
13 Type 'contributors()' for more information and
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
14 'citation()' on how to cite R or R packages in publications.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
15
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
16 Type 'demo()' for some demos, 'help()' for on-line help, or
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
17 'help.start()' for an HTML browser interface to help.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
18 Type 'q()' to quit R.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
19
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
20 > ## Feature Selection ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
21 > get_features <- function(myGenes, f="gene") {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
22 + if (f == "isoforms")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
23 + return(isoforms(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
24 + else if (f == "tss")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
25 + return(TSS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
26 + else if (f == "cds")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
27 + return(CDS(myGenes))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
28 + else
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
29 + return(myGenes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
30 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
31 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
32 > ## Main Function ##
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
33 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
34 > library(argparse)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
35 Loading required package: proto
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
36 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
37 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
38 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
54 > parser$add_argument('--features', dest='features', action="store", default="genes")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
56 > parser$add_argument('--iter_max', dest='iter_max', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
57 > parser$add_argument('--genes', dest='genes', action="append")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
58 > parser$add_argument('--k', dest='k', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
59 > parser$add_argument('--x', dest='x', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
60 > parser$add_argument('--y', dest='y', action="store")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
61 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
62 > args <- parser$parse_args()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
63 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
64 > print(args)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
65 $border
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
66 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
67
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
68 $clustering
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
69 [1] "both"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
70
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
71 $count
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
72 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
73
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
74 $error_bars
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
75 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
76
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
77 $features
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
78 [1] "genes"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
79
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
80 $filename
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
81 [1] "plot-fpkmSCV-0.png"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
82
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
83 $gene_selector
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
84 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
85
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
86 $genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
87 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
88
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
89 $height
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
90 [1] 960
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
91
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
92 $input_database
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
93 [1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_49.dat"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
94
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
95 $iter_max
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
96 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
97
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
98 $k
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
99 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
100
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
101 $labcol
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
102 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
103
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
104 $labrow
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
105 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
106
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
107 $log10
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
108 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
109
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
110 $plotType
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
111 [1] "fpkmSCV"
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
112
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
113 $replicates
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
114 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
115
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
116 $smooth
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
117 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
118
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
119 $summary
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
120 [1] FALSE
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
121
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
122 $width
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
123 [1] 1280
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
124
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
125 $x
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
126 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
127
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
128 $y
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
129 NULL
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
130
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
131 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
132 > #q()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
133 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
134 > ## Load cummeRbund library
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
135 > library("cummeRbund")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
136 Loading required package: BiocGenerics
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
137 Loading required package: parallel
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
138
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
139 Attaching package: ‘BiocGenerics’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
140
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
141 The following objects are masked from ‘package:parallel’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
142
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
144 clusterExport, clusterMap, parApply, parCapply, parLapply,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
145 parLapplyLB, parRapply, parSapply, parSapplyLB
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
146
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
147 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
148
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
149 xtabs
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
150
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
151 The following objects are masked from ‘package:base’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
152
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
157 rownames, sapply, setdiff, sort, table, tapply, union, unique,
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
158 unlist, unsplit
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
159
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
160 Loading required package: RSQLite
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
161 Loading required package: DBI
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
162 Loading required package: ggplot2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
163 Loading required package: reshape2
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
164 Loading required package: fastcluster
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
165
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
166 Attaching package: ‘fastcluster’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
167
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
168 The following object is masked from ‘package:stats’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
169
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
170 hclust
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
171
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
172 Loading required package: rtracklayer
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
173 Loading required package: GenomicRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
174 Loading required package: S4Vectors
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
175 Loading required package: stats4
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
176 Loading required package: IRanges
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
177 Loading required package: GenomeInfoDb
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
178 Loading required package: Gviz
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
179 Loading required package: grid
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
180
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
181 Attaching package: ‘cummeRbund’
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
182
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
183 The following object is masked from ‘package:GenomicRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
184
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
185 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
186
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
187 The following object is masked from ‘package:IRanges’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
188
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
189 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
190
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
191 The following object is masked from ‘package:BiocGenerics’:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
192
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
193 conditions
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
194
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
195 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
196 > ## Initialize cuff object
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
198 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
199 > ## Print out info
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
200 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
201 CuffSet instance with:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
202 2 samples
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
203 87 genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
204 90 isoforms
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
205 88 TSS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
206 0 CDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
207 87 promoters
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
208 88 splicing
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
209 0 relCDS
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
210 > sink("cuffdb_info.txt")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
211 > print(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
212 > print("SAMPLES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
213 > samples(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
214 > print("REPLICATES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
215 > replicates(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
216 > print("FEATURES:")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
217 > print(annotation(genes(cuff)))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
218 > cat(annotation(genes(cuff))[[1]],sep=",")
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
219 > sink()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
220 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
222 > tryCatch({
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
223 + if (args$plotType == 'density') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
225 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
226 + else if (args$plotType == 'boxplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
228 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
229 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
230 + MDSplot(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
231 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
232 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
234 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
235 + else if (args$plotType == 'dendrogram') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
236 + csDendro(genes(cuff), replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
237 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
238 + else if (args$plotType == 'scatter') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
239 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
240 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
242 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
243 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
245 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
246 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
247 + else if (args$plotType == 'volcano') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
248 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
250 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
251 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
252 + myGenes <- genes(cuff)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
253 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
254 + csVolcano(myGenes, args$x, args$y)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
255 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
256 + else if (args$plotType == 'heatmap') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
257 + if (args$gene_selector) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
258 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
259 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
260 + else {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
262 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
264 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
265 + else if (args$plotType == 'cluster') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
266 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
267 + csCluster(get_features(myGenes, args$features), k=args$k)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
268 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
269 + else if (args$plotType == 'dispersion') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
270 + dispersionPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
271 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
272 + else if (args$plotType == 'fpkmSCV') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
273 + fpkmSCVPlot(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
274 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
275 + else if (args$plotType == 'scatterMatrix') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
276 + csScatterMatrix(genes(cuff))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
277 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
278 + else if (args$plotType == 'expressionplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
279 + myGenes <- getGenes(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
281 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
282 + else if (args$plotType == 'expressionbarplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
283 + myGeneId <- args$genes
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
284 + myGenes <- getGenes(cuff, myGeneId)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
286 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
287 + else if (args$plotType == 'mds') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
288 + MDSplot(genes(cuff),replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
289 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
290 + else if (args$plotType == 'pca') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
292 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
293 + else if (args$plotType == 'maplot') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
295 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
296 + else if (args$plotType == 'genetrack') {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
297 + myGene <- getGene(cuff, args$genes)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
298 + plotTracks(makeGeneRegionTrack(myGene))
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
299 + }
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
300 + },error = function(e) {
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
301 + write(paste("Failed:", e, sep=" "), stderr())
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
302 + q("no", 1, TRUE)
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
303 + })
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
304 Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
305 geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
306 Fontconfig error: Cannot load default config file
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
307 Warning message:
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
308 In .local(object, FPKMLowerBound, ...) :
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
309 At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead.
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
310 > devname = dev.off()
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
311 >
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
312 > #end for
587c425b4e76 Initial commit with version 1.0.0 of the cummeRbund wrapper.
devteam
parents:
diff changeset
313 >