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annotate test-data/heatmap.txt @ 0:587c425b4e76 draft

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Initial commit with version 1.0.0 of the cummeRbund wrapper.
author devteam
date Tue, 23 Dec 2014 15:58:27 -0500
parents
children 78fcfc04fcfe
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1
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2 R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
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3 Copyright (C) 2014 The R Foundation for Statistical Computing
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4 Platform: x86_64-unknown-linux-gnu (64-bit)
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5
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6 R is free software and comes with ABSOLUTELY NO WARRANTY.
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7 You are welcome to redistribute it under certain conditions.
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8 Type 'license()' or 'licence()' for distribution details.
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9
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10 Natural language support but running in an English locale
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11
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12 R is a collaborative project with many contributors.
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13 Type 'contributors()' for more information and
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14 'citation()' on how to cite R or R packages in publications.
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15
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16 Type 'demo()' for some demos, 'help()' for on-line help, or
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17 'help.start()' for an HTML browser interface to help.
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18 Type 'q()' to quit R.
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19
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20 > ## Feature Selection ##
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21 > get_features <- function(myGenes, f="gene") {
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22 + if (f == "isoforms")
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23 + return(isoforms(myGenes))
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24 + else if (f == "tss")
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25 + return(TSS(myGenes))
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26 + else if (f == "cds")
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27 + return(CDS(myGenes))
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28 + else
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29 + return(myGenes)
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30 + }
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31 >
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32 > ## Main Function ##
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33 >
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34 > library(argparse)
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35 Loading required package: proto
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36 >
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37 > parser <- ArgumentParser(description='Create a plot with cummeRbund')
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38 >
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39 > parser$add_argument('--type', dest='plotType', default='Density', required=TRUE)
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40 > parser$add_argument('--height', dest='height', type='integer', default=960, required=TRUE)
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41 > parser$add_argument('--width', dest='width', type='integer', default=1280, required=TRUE)
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42 > parser$add_argument('--outfile', dest='filename', default="plot-unknown-0.png", required=TRUE)
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43 > parser$add_argument('--input', dest='input_database', default="cuffData.db", required=TRUE)
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44 > parser$add_argument('--smooth', dest='smooth', action="store_true", default=FALSE)
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45 > parser$add_argument('--gene_selector', dest='gene_selector', action="store_true", default=FALSE)
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46 > parser$add_argument('--replicates', dest='replicates', action="store_true", default=FALSE)
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47 > parser$add_argument('--labcol', dest='labcol', action="store_true", default=FALSE)
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48 > parser$add_argument('--labrow', dest='labrow', action="store_true", default=FALSE)
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49 > parser$add_argument('--border', dest='border', action="store_true", default=FALSE)
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50 > parser$add_argument('--summary', dest='summary', action="store_true", default=FALSE)
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51 > parser$add_argument('--count', dest='count', action="store_true", default=FALSE)
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52 > parser$add_argument('--error_bars', dest='error_bars', action="store_true", default=FALSE)
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53 > parser$add_argument('--log10', dest='log10', action="store_true", default=FALSE)
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54 > parser$add_argument('--features', dest='features', action="store", default="genes")
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55 > parser$add_argument('--clustering', dest='clustering', action="store", default="both")
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56 > parser$add_argument('--iter_max', dest='iter_max', action="store")
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57 > parser$add_argument('--genes', dest='genes', action="append")
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58 > parser$add_argument('--k', dest='k', action="store")
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59 > parser$add_argument('--x', dest='x', action="store")
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60 > parser$add_argument('--y', dest='y', action="store")
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61 >
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62 > args <- parser$parse_args()
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63 >
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64 > print(args)
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65 $border
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66 [1] FALSE
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67
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68 $clustering
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69 [1] "both"
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70
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71 $count
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72 [1] FALSE
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73
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74 $error_bars
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75 [1] FALSE
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76
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77 $features
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78 [1] "gene"
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79
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80 $filename
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81 [1] "plot-heatmap-0.png"
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82
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83 $gene_selector
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84 [1] FALSE
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85
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86 $genes
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87 [1] "XLOC_000078"
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88
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89 $height
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90 [1] 960
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91
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92 $input_database
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93 [1] "/tmp/tmpCu9yWT/tmpPy7OpW/database/files/000/dataset_22.dat"
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94
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95 $iter_max
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96 NULL
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97
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98 $k
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99 NULL
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100
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101 $labcol
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102 [1] TRUE
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103
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104 $labrow
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105 [1] TRUE
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106
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107 $log10
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108 [1] TRUE
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109
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110 $plotType
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111 [1] "heatmap"
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112
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113 $replicates
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114 [1] FALSE
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115
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116 $smooth
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117 [1] FALSE
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118
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119 $summary
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120 [1] FALSE
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121
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122 $width
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123 [1] 1280
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124
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125 $x
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126 NULL
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127
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128 $y
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129 NULL
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130
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131 >
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132 > #q()
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133 >
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134 > ## Load cummeRbund library
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135 > library("cummeRbund")
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136 Loading required package: BiocGenerics
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137 Loading required package: parallel
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138
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139 Attaching package: ‘BiocGenerics’
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140
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141 The following objects are masked from ‘package:parallel’:
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142
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143 clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
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144 clusterExport, clusterMap, parApply, parCapply, parLapply,
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145 parLapplyLB, parRapply, parSapply, parSapplyLB
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146
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147 The following object is masked from ‘package:stats’:
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148
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149 xtabs
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150
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151 The following objects are masked from ‘package:base’:
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152
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153 anyDuplicated, append, as.data.frame, as.vector, cbind, colnames,
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154 do.call, duplicated, eval, evalq, Filter, Find, get, intersect,
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155 is.unsorted, lapply, Map, mapply, match, mget, order, paste, pmax,
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156 pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce, rep.int,
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157 rownames, sapply, setdiff, sort, table, tapply, union, unique,
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158 unlist, unsplit
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159
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160 Loading required package: RSQLite
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161 Loading required package: DBI
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162 Loading required package: ggplot2
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163 Loading required package: reshape2
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164 Loading required package: fastcluster
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165
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166 Attaching package: ‘fastcluster’
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167
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168 The following object is masked from ‘package:stats’:
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169
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170 hclust
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171
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172 Loading required package: rtracklayer
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173 Loading required package: GenomicRanges
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174 Loading required package: S4Vectors
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175 Loading required package: stats4
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176 Loading required package: IRanges
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177 Loading required package: GenomeInfoDb
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178 Loading required package: Gviz
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179 Loading required package: grid
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180
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181 Attaching package: ‘cummeRbund’
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182
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183 The following object is masked from ‘package:GenomicRanges’:
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184
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185 promoters
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186
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187 The following object is masked from ‘package:IRanges’:
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188
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189 promoters
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190
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191 The following object is masked from ‘package:BiocGenerics’:
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192
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193 conditions
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194
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195 >
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196 > ## Initialize cuff object
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197 > cuff <- readCufflinks(dir = "", dbFile = args$input_database, rebuild = FALSE)
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198 >
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199 > ## Print out info
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200 > print(cuff)
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201 CuffSet instance with:
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202 2 samples
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203 87 genes
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204 90 isoforms
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205 88 TSS
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206 0 CDS
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207 87 promoters
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208 88 splicing
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209 0 relCDS
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210 > sink("cuffdb_info.txt")
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211 > print(cuff)
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212 > print("SAMPLES:")
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213 > samples(cuff)
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214 > print("REPLICATES:")
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215 > replicates(cuff)
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216 > print("FEATURES:")
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217 > print(annotation(genes(cuff)))
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218 > cat(annotation(genes(cuff))[[1]],sep=",")
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219 > sink()
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220 >
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221 > png(filename = args$filename, width = args$width, height = args$height, type=c('cairo-png'))
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222 > tryCatch({
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223 + if (args$plotType == 'density') {
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224 + csDensity(genes(cuff), replicates=args$replicates, logMode=args$log10)
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225 + }
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226 + else if (args$plotType == 'boxplot') {
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227 + csBoxplot(genes(cuff), replicates=args$replicates, logMode=args$log10)
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228 + }
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229 + else if (args$plotType == 'mds') {
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230 + MDSplot(genes(cuff), replicates=args$replicates)
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231 + }
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232 + else if (args$plotType == 'pca') {
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233 + PCAplot(genes(cuff), "PC1", "PC2", replicates=args$replicates)
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234 + }
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235 + else if (args$plotType == 'dendrogram') {
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236 + csDendro(genes(cuff), replicates=args$replicates)
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237 + }
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238 + else if (args$plotType == 'scatter') {
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239 + if (args$gene_selector) {
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240 + myGenes <- getGenes(cuff, args$genes)
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241 + csScatter(get_features(myGenes, args$features), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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242 + }
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243 + else {
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244 + csScatter(genes(cuff), args$x, args$y, smooth=args$smooth, logMode=args$log10)
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245 + }
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246 + }
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247 + else if (args$plotType == 'volcano') {
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248 + if (args$gene_selector) {
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249 + myGenes <- get_features(getGenes(cuff, args$genes), args$features)
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250 + }
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251 + else {
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252 + myGenes <- genes(cuff)
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253 + }
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254 + csVolcano(myGenes, args$x, args$y)
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255 + }
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256 + else if (args$plotType == 'heatmap') {
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257 + if (args$gene_selector) {
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258 + myGenes <- getGenes(cuff, args$genes)
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259 + }
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260 + else {
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261 + myGenes <- getGenes(cuff,annotation(genes(cuff))[[1]])
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262 + }
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263 + csHeatmap(get_features(myGenes, args$features), clustering=args$clustering, labCol=args$labcol, labRow=args$labrow, border=args$border, logMode=args$log10)
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264 + }
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265 + else if (args$plotType == 'cluster') {
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266 + myGenes <- getGenes(cuff, args$genes)
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267 + csCluster(get_features(myGenes, args$features), k=args$k)
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268 + }
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269 + else if (args$plotType == 'dispersion') {
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270 + dispersionPlot(genes(cuff))
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271 + }
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272 + else if (args$plotType == 'fpkmSCV') {
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273 + fpkmSCVPlot(genes(cuff))
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274 + }
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275 + else if (args$plotType == 'scatterMatrix') {
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276 + csScatterMatrix(genes(cuff))
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277 + }
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278 + else if (args$plotType == 'expressionplot') {
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279 + myGenes <- getGenes(cuff, args$genes)
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280 + expressionPlot(get_features(myGenes, args$features), drawSummary=args$summary, showErrorbars=args$error_bars, replicates=args$replicates)
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281 + }
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282 + else if (args$plotType == 'expressionbarplot') {
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283 + myGeneId <- args$genes
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284 + myGenes <- getGenes(cuff, myGeneId)
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285 + expressionBarplot(get_features(myGenes, args$features), showErrorbars=args$error_bars, replicates=args$replicates)
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286 + }
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287 + else if (args$plotType == 'mds') {
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288 + MDSplot(genes(cuff),replicates=args$replicates)
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289 + }
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290 + else if (args$plotType == 'pca') {
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291 + PCAplot(genes(cuff),"PC1","PC2", replicates=args$replicates)
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292 + }
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293 + else if (args$plotType == 'maplot') {
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294 + MAplot(genes(cuff), args$x, args$y, useCount=args$count)
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295 + }
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296 + else if (args$plotType == 'genetrack') {
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297 + myGene <- getGene(cuff, args$genes)
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298 + plotTracks(makeGeneRegionTrack(myGene))
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299 + }
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300 + },error = function(e) {
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301 + write(paste("Failed:", e, sep=" "), stderr())
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302 + q("no", 1, TRUE)
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303 + })
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304 Getting gene information:
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305 FPKM
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306 Differential Expression Data
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307 Annotation Data
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308 Replicate FPKMs
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309 Counts
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310 Getting isoforms information:
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311 FPKM
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312 Differential Expression Data
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313 Annotation Data
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314 Replicate FPKMs
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315 Counts
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316 Getting CDS information:
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317 FPKM
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318 Differential Expression Data
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319 Annotation Data
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320 Replicate FPKMs
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321 Counts
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322 Getting TSS information:
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323 FPKM
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324 Differential Expression Data
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325 Annotation Data
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326 Replicate FPKMs
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327 Counts
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328 Getting promoter information:
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329 distData
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330 Getting splicing information:
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331 distData
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332 Getting relCDS information:
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333 distData
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334 Using tracking_id, sample_name as id variables
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335 No id variables; using all as measure variables
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336 Fontconfig error: Cannot load default config file
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337 > devname = dev.off()
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338 >
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339 > #end for
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340 >