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comparison test-data/fpkmSCV.txt @ 5:78fcfc04fcfe draft

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/cummerbund commit f3f0bef4a450aafab3c6b05a27647471f93b22f3
author devteam
date Thu, 23 Feb 2017 20:24:03 -0500
parents 587c425b4e76
children
comparison
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4:ba8fde59843d 5:78fcfc04fcfe
1
2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
3 Copyright (C) 2014 The R Foundation for Statistical Computing
4 Platform: x86_64-unknown-linux-gnu (64-bit)
5
6 R is free software and comes with ABSOLUTELY NO WARRANTY.
7 You are welcome to redistribute it under certain conditions.
8 Type 'license()' or 'licence()' for distribution details.
9
10 Natural language support but running in an English locale
11
12 R is a collaborative project with many contributors.
13 Type 'contributors()' for more information and
14 'citation()' on how to cite R or R packages in publications.
15
16 Type 'demo()' for some demos, 'help()' for on-line help, or
17 'help.start()' for an HTML browser interface to help.
18 Type 'q()' to quit R.
19
20 > ## Feature Selection ##
21 > get_features <- function(myGenes, f="gene") { 1 > get_features <- function(myGenes, f="gene") {
22 + if (f == "isoforms") 2 + if (f == "isoforms")
23 + return(isoforms(myGenes)) 3 + return(isoforms(myGenes))
24 + else if (f == "tss") 4 + else if (f == "tss")
25 + return(TSS(myGenes)) 5 + return(TSS(myGenes))
59 > parser$add_argument('--x', dest='x', action="store") 39 > parser$add_argument('--x', dest='x', action="store")
60 > parser$add_argument('--y', dest='y', action="store") 40 > parser$add_argument('--y', dest='y', action="store")
61 > 41 >
62 > args <- parser$parse_args() 42 > args <- parser$parse_args()
63 > 43 >
64 > print(args)
65 $border
66 [1] FALSE
67
68 $clustering
69 [1] "both"
70
71 $count
72 [1] FALSE
73
74 $error_bars
75 [1] FALSE
76
77 $features
78 [1] "genes"
79
80 $filename
81 [1] "plot-fpkmSCV-0.png"
82
83 $gene_selector
84 [1] FALSE
85
86 $genes
87 NULL
88
89 $height
90 [1] 960
91
92 $input_database
93 [1] "/tmp/tmp3exXG8/tmpuNktUy/database/files/000/dataset_49.dat"
94
95 $iter_max
96 NULL
97
98 $k
99 NULL
100
101 $labcol
102 [1] FALSE
103
104 $labrow
105 [1] FALSE
106
107 $log10
108 [1] FALSE
109
110 $plotType
111 [1] "fpkmSCV"
112
113 $replicates
114 [1] FALSE
115
116 $smooth
117 [1] FALSE
118
119 $summary
120 [1] FALSE
121
122 $width
123 [1] 1280
124
125 $x
126 NULL
127
128 $y
129 NULL
130
131 >
132 > #q()
133 >
134 > ## Load cummeRbund library 44 > ## Load cummeRbund library
135 > library("cummeRbund") 45 > library("cummeRbund")
136 Loading required package: BiocGenerics 46 Loading required package: BiocGenerics
47 Loading required package: methods
137 Loading required package: parallel 48 Loading required package: parallel
138 49
139 Attaching package: ‘BiocGenerics’ 50 Attaching package: ‘BiocGenerics’
140 51
141 The following objects are masked from ‘package:parallel’: 52 The following objects are masked from ‘package:parallel’:
142 53
143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, 54 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
144 clusterExport, clusterMap, parApply, parCapply, parLapply, 55 clusterExport, clusterMap, parApply, parCapply, parLapply,
145 parLapplyLB, parRapply, parSapply, parSapplyLB 56 parLapplyLB, parRapply, parSapply, parSapplyLB
146 57
147 The following object is masked from ‘package:stats’: 58 The following objects are masked from ‘package:stats’:
148 59
149 xtabs 60 IQR, mad, xtabs
150 61
151 The following objects are masked from ‘package:base’: 62 The following objects are masked from ‘package:base’:
152 63
153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames, 64 anyDuplicated, append, as.data.frame, cbind, colnames, do.call,
154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect, 65 duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect,
155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax, 66 is.unsorted, lapply, lengths, Map, mapply, match, mget, order,
156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int, 67 paste, pmax, pmax.int, pmin, pmin.int, Position, rank, rbind,
157 rownames, sapply, setdiff, sort, table, tapply, union, unique, 68 Reduce, rownames, sapply, setdiff, sort, table, tapply, union,
158 unlist, unsplit 69 unique, unsplit, which, which.max, which.min
159 70
160 Loading required package: RSQLite 71 Loading required package: RSQLite
161 Loading required package: DBI 72 Loading required package: DBI
162 Loading required package: ggplot2 73 Loading required package: ggplot2
163 Loading required package: reshape2 74 Loading required package: reshape2
169 80
170 hclust 81 hclust
171 82
172 Loading required package: rtracklayer 83 Loading required package: rtracklayer
173 Loading required package: GenomicRanges 84 Loading required package: GenomicRanges
85 Loading required package: stats4
174 Loading required package: S4Vectors 86 Loading required package: S4Vectors
175 Loading required package: stats4 87
88 Attaching package: ‘S4Vectors’
89
90 The following objects are masked from ‘package:base’:
91
92 colMeans, colSums, expand.grid, rowMeans, rowSums
93
176 Loading required package: IRanges 94 Loading required package: IRanges
177 Loading required package: GenomeInfoDb 95 Loading required package: GenomeInfoDb
178 Loading required package: Gviz 96 Loading required package: Gviz
179 Loading required package: grid 97 Loading required package: grid
98 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
99 by .GlobalEnv when processing object ‘plot.index’
100 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
101 by .GlobalEnv when processing object ‘plot.index’
102 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
103 by .GlobalEnv when processing object ‘plot.index’
104 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
105 by .GlobalEnv when processing object ‘plot.index’
106 Warning: namespace ‘ensembldb’ is not available and has been replaced
107 by .GlobalEnv when processing object ‘plot.index’
108 Warning: namespace ‘ensembldb’ is not available and has been replaced
109 by .GlobalEnv when processing object ‘plot.index’
110 Warning: namespace ‘ensembldb’ is not available and has been replaced
111 by .GlobalEnv when processing object ‘plot.index’
112 Warning: namespace ‘ensembldb’ is not available and has been replaced
113 by .GlobalEnv when processing object ‘plot.index’
114 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
115 by .GlobalEnv when processing object ‘plot.index’
116 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
117 by .GlobalEnv when processing object ‘plot.index’
118 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
119 by .GlobalEnv when processing object ‘plot.index’
120 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
121 by .GlobalEnv when processing object ‘plot.index’
122 Warning: namespace ‘ensembldb’ is not available and has been replaced
123 by .GlobalEnv when processing object ‘plot.index’
124 Warning: namespace ‘ensembldb’ is not available and has been replaced
125 by .GlobalEnv when processing object ‘plot.index’
126 Warning: namespace ‘ensembldb’ is not available and has been replaced
127 by .GlobalEnv when processing object ‘plot.index’
128 Warning: namespace ‘ensembldb’ is not available and has been replaced
129 by .GlobalEnv when processing object ‘plot.index’
130 Warning: namespace ‘ensembldb’ is not available and has been replaced
131 by .GlobalEnv when processing object ‘plot.index’
132 Warning: namespace ‘ensembldb’ is not available and has been replaced
133 by .GlobalEnv when processing object ‘plot.index’
134 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
135 by .GlobalEnv when processing object ‘plot.index’
136 Warning: namespace ‘ensembldb’ is not available and has been replaced
137 by .GlobalEnv when processing object ‘plot.index’
138 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
139 by .GlobalEnv when processing object ‘plot.index’
140 Warning: namespace ‘ensembldb’ is not available and has been replaced
141 by .GlobalEnv when processing object ‘plot.index’
142 Warning: namespace ‘ensembldb’ is not available and has been replaced
143 by .GlobalEnv when processing object ‘plot.index’
144 Warning: namespace ‘ensembldb’ is not available and has been replaced
145 by .GlobalEnv when processing object ‘plot.index’
146 Warning: namespace ‘ensembldb’ is not available and has been replaced
147 by .GlobalEnv when processing object ‘plot.index’
148 Warning: namespace ‘ensembldb’ is not available and has been replaced
149 by .GlobalEnv when processing object ‘plot.index’
150 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
151 by .GlobalEnv when processing object ‘plot.index’
152 Warning: namespace ‘AnnotationHub’ is not available and has been replaced
153 by .GlobalEnv when processing object ‘plot.index’
180 154
181 Attaching package: ‘cummeRbund’ 155 Attaching package: ‘cummeRbund’
182 156
183 The following object is masked from ‘package:GenomicRanges’: 157 The following object is masked from ‘package:GenomicRanges’:
184 158
299 + } 273 + }
300 + },error = function(e) { 274 + },error = function(e) {
301 + write(paste("Failed:", e, sep=" "), stderr()) 275 + write(paste("Failed:", e, sep=" "), stderr())
302 + q("no", 1, TRUE) 276 + q("no", 1, TRUE)
303 + }) 277 + })
304 Scale for 'x' is already present. Adding another scale for 'x', which will replace the existing scale. 278 Scale for 'x' is already present. Adding another scale for 'x', which will
305 geom_smooth: method="auto" and size of largest group is <1000, so using loess. Use 'method = x' to change the smoothing method. 279 replace the existing scale.
306 Fontconfig error: Cannot load default config file 280 `geom_smooth()` using method = 'loess'
307 Warning message: 281 Warning message:
308 In .local(object, FPKMLowerBound, ...) : 282 In .local(object, FPKMLowerBound, ...) :
309 At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead. 283 At least one of your conditions does not have enough replicates to estimate variance. Estimating variance across all conditions instead.
310 > devname = dev.off() 284 > devname = dev.off()
311 > 285 >
312 > #end for
313 >