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2
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1 setwd("/Volumes/BINF1_Raid/home/dtanwar/projects/H3K4me3_McMasterU/exp/20171026-GO_analysis_232_changed_genes-11/20171027-ranked_genes_232")
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2 table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
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3 stringsAsFactors = F)
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4 View(table)
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5 table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
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6 stringsAsFactors = F)[,c(22,7)]
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7 View(table)
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8 sp_table <- split(x = table, f = table$SYMBOL)
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9 genes <- lapply(sp_table, function(x){
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10 a <- x[1,]
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11 a[,2] <- mean(x[,2])
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12 return(a)
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13 })
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14 library(plyr)
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15 gl <- ldply(genes, data.frame)
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16 View(gl)
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17 gl <- ldply(genes, data.frame)[,-1]
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18 View(gl)
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19 gl[,1] <- toupper(gl[,1])
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20 View(gl)
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21 write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
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22 setwd("/Volumes/BINF1_Raid/home/dtanwar/projects/H3K4me3_McMasterU/exp/20171026-GO_analysis_232_changed_genes-11/20171027-01_ranked_genes_232")
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23 library(plyr)
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24 table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
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25 stringsAsFactors = F)[,c(22,7)]
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26 sp_table <- split(x = table, f = table$SYMBOL)
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27 genes <- lapply(sp_table, function(x){
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28 a <- x[1,]
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29 a[,2] <- mean(x[,2])
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30 return(a)
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31 })
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32 gl <- ldply(genes, data.frame)[,-1]
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33 write.table(gl, "./output/20171029-original_ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
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34 gl[,1] <- toupper(gl[,1])
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35 write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
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36 library(plyr)
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37 table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
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38 stringsAsFactors = F)[,c(22,7)]
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39 sp_table <- split(x = table, f = table$SYMBOL)
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40 genes <- lapply(sp_table, function(x){
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41 a <- x[1,]
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42 a[,2] <- mean(x[,2])
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43 return(a)
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44 })
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45 gl <- ldply(genes, data.frame)[,-1]
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46 gl
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47 write.table(gl, "./output/20171029-original_ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
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48 gl[,1] <- toupper(gl[,1])
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49 write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
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50 # Send R errors to stderr
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51 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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52 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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53 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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54 # Import libraries
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55 library("GenomicRanges")
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56 source("https://bioconductor.org/biocLite.R")
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57 biocLite()
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58 source("http://bioconductor.org/biocLite.R")
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59 biocLite()
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60 library("getopt")
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61 library("edgeR")
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62 library("openxlsx")
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63 library("data.table")
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64 biocLite("getopt")
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65 # biocLite("openxlsx")
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66 biocLite("data.table")
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67 # Send R errors to stderr
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68 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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69 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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70 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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71 library("getopt")
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72 library("edgeR")
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73 biocLite("getopt")
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74 source("http://bioconductor.org/biocLite.R")
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75 biocLite()
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76 biocLite("edgeR")
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77 biocLite("edgeR")
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78 biocLite("Rcpp")
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79 biocLite("limma")
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80 biocLite("edgeR")
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81 biocLite("edgeR")
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82 source("http://bioconductor.org/biocLite.R")
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83 biocLite()
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84 biocLite("edgeR")
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85 biocLite("GenomicRanges")
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86 biocLite("Rsamtools")
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87 # Import libraries
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88 library("GenomicRanges")
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89 library("Rsamtools")
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90 library("rtracklayer")
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91 library("parallel")
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92 library("foreach")
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93 library("doParallel")
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94 library("GenomicFeatures")
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95 library("Gviz")
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96 library("getopt")
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97 library("data.table")
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98 library("BSgenome")
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99 library("Biobase")
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100 library("iterators")
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101 library("Biostrings")
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102 library("IRanges")
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103 library("BiocGenerics")
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104 library("AnnotationDbi")
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105 library("XVector")
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106 library("GenomeInfoDb")
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107 library("S4Vectors")
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108 library("GenomicAlignments")
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109 library("BSgenome.Hsapiens.UCSC.hg19")
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110 library("org.Hs.eg.db")
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111 library("BSgenome.Mmusculus.UCSC.mm10")
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112 library("org.Mm.eg.db")
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113 library("getopt")
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114 library("edgeR")
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115 # library("openxlsx")
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116 library("data.table")
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117 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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118 source("https://bioconductor.org/biocLite.R")
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119 biocLite()
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120 source("https://bioconductor.org/biocLite.R")
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121 biocLite()
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122 library("getopt")
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123 library("edgeR")
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124 # library("openxlsx")
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125 library("data.table")
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126 source("https://bioconductor.org/biocLite.R")
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127 biocLite("edgeR")
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128 library("getopt")
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129 library("edgeR")
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130 # library("openxlsx")
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131 library("data.table")
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132 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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133 # Take in trailing command line arguments
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134 args <- commandArgs(trailingOnly = TRUE)
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135 # Get options using the spec as defined by the enclosed list
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136 # Options are read from the default: commandArgs(TRUE)
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137 option_specification = matrix(c(
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138 'input1', 'i1', 2, 'character',
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139 'input2', 'i2', 2, 'character',
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140 'input3', 'i3', 2, 'integer',
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141 'input4', 'i4', 2, 'integer',
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142 'output', 'o', 2, 'character'
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143 ), byrow=TRUE, ncol=4);
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144 # Parse options
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145 options = getopt(option_specification)
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146 library("rworldmap")
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147 install.packages("rworldmap")
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148 library("rworldmap")
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149 theCountries <- c("DEU", "COD", "BFA")
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150 malDF <- data.frame(country = c("DEU", "COD", "BFA"),
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151 malaria = c(1, 1, 1))
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152 malMap <- joinCountryData2Map(malDF, joinCode = "ISO3",
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153 nameJoinColumn = "country")
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154 mapCountryData(malMap, nameColumnToPlot="malaria", catMethod = "categorical",
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155 missingCountryCol = gray(.8))
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156 require(rgdal)
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157 require(rgeos)
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158 require(ggplot2)
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159 install.packages("rgdal")
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160 install.packages("rgeos")
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161 require(rgdal)
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162 require(rgeos)
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163 require(ggplot2)
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164 655 + 290 + 658
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165 235+38+186
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166 370+357+50+37+59+386+30+112+300
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167 750+22+49+25+317
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168 750+22+49+25+317 +6
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169 239 + 61+760
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170 1060+1169+1701
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171 235+38+186
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172 3930+459
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173 653+571+546+211+
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174 0
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175 1981+1235+1148
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176 4364+43
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177 1701-40
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178 459+1661+1060
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179 459+1661+1060 +1169
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180 459-27
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181 370+205+6+179+360+455
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182 432+1575+1060+1169
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183 mat <- matrix(data = c(1:9), nrow = 3, ncol = 3, byrow = T)
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184 mat
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185 apply(mat, 1, mean)
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186 apply(mat, 2, mean)
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187 vec <- 1:10
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188 apply(X = vec, 1, print)
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189 apply(X = vec, 2, print)
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190 sapply(X = vec, FUN = print)
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191 sapply(X = vec, FUN = print, simplify = T)
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192 sapply(X = vec, FUN = print, simplify = F)
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193 sapply(X = vec, FUN = function(x) x -1)
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194 as.integer(c(4.1, 5.2, 6.3, 6.4))
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195 as.numeric(c(4.1, 5.2, 6.3, 6.4))
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196 ?quantile
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197 ?read.table
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198 ?hist
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199 ?boxplot
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200 ?read.csv
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201 ?quantile
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202 quantile(x <- rnorm(1001)) # Extremes & Quartiles by default
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203 res <- matrix(as.numeric(NA), 9, 7)
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204 res
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205 for(type in 1:9) res[type, ] <- y <- quantile(x, p, type = type)
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206 dimnames(res) <- list(1:9, names(y))
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207 for(type in 1:9) res[type, ] <- y <- quantile(x, p, type = type)
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208 setwd("~/Desktop/planemo_tools/16_fgsea")
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209 # Send R errors to stderr
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210 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
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211 # Avoid crashing Galaxy with an UTF8 error on German LC settings
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212 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
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213 # Import library
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214 library("getopt")
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215 library("fgsea")
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216 options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
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217 # Take in trailing command line arguments
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218 args <- commandArgs(trailingOnly = TRUE)
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219 sessionInfo()
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