--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/16_fgsea/.Rhistory	Mon Dec 11 09:52:26 2017 -0500
@@ -0,0 +1,219 @@
+setwd("/Volumes/BINF1_Raid/home/dtanwar/projects/H3K4me3_McMasterU/exp/20171026-GO_analysis_232_changed_genes-11/20171027-ranked_genes_232")
+table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
+stringsAsFactors = F)
+View(table)
+table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
+stringsAsFactors = F)[,c(22,7)]
+View(table)
+sp_table <- split(x = table, f = table$SYMBOL)
+genes <- lapply(sp_table, function(x){
+a <- x[1,]
+a[,2] <- mean(x[,2])
+return(a)
+})
+library(plyr)
+gl <- ldply(genes, data.frame)
+View(gl)
+gl <- ldply(genes, data.frame)[,-1]
+View(gl)
+gl[,1] <- toupper(gl[,1])
+View(gl)
+write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
+setwd("/Volumes/BINF1_Raid/home/dtanwar/projects/H3K4me3_McMasterU/exp/20171026-GO_analysis_232_changed_genes-11/20171027-01_ranked_genes_232")
+library(plyr)
+table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
+stringsAsFactors = F)[,c(22,7)]
+sp_table <- split(x = table, f = table$SYMBOL)
+genes <- lapply(sp_table, function(x){
+a <- x[1,]
+a[,2] <- mean(x[,2])
+return(a)
+})
+gl <- ldply(genes, data.frame)[,-1]
+write.table(gl, "./output/20171029-original_ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
+gl[,1] <- toupper(gl[,1])
+write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
+library(plyr)
+table <- read.delim("./input/20170722-genes_info_TSS_500bp.txt.xz", sep = "\t", header = T,
+stringsAsFactors = F)[,c(22,7)]
+sp_table <- split(x = table, f = table$SYMBOL)
+genes <- lapply(sp_table, function(x){
+a <- x[1,]
+a[,2] <- mean(x[,2])
+return(a)
+})
+gl <- ldply(genes, data.frame)[,-1]
+gl
+write.table(gl, "./output/20171029-original_ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
+gl[,1] <- toupper(gl[,1])
+write.table(gl, "./output/ranked_genes_list_232.rnk", quote = F, sep = "\t", row.names = F, col.names = F)
+# Send R errors to stderr
+options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+# Import libraries
+library("GenomicRanges")
+source("https://bioconductor.org/biocLite.R")
+biocLite()
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+library("getopt")
+library("edgeR")
+library("openxlsx")
+library("data.table")
+biocLite("getopt")
+# biocLite("openxlsx")
+biocLite("data.table")
+# Send R errors to stderr
+options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+library("getopt")
+library("edgeR")
+biocLite("getopt")
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+biocLite("edgeR")
+biocLite("edgeR")
+biocLite("Rcpp")
+biocLite("limma")
+biocLite("edgeR")
+biocLite("edgeR")
+source("http://bioconductor.org/biocLite.R")
+biocLite()
+biocLite("edgeR")
+biocLite("GenomicRanges")
+biocLite("Rsamtools")
+# Import libraries
+library("GenomicRanges")
+library("Rsamtools")
+library("rtracklayer")
+library("parallel")
+library("foreach")
+library("doParallel")
+library("GenomicFeatures")
+library("Gviz")
+library("getopt")
+library("data.table")
+library("BSgenome")
+library("Biobase")
+library("iterators")
+library("Biostrings")
+library("IRanges")
+library("BiocGenerics")
+library("AnnotationDbi")
+library("XVector")
+library("GenomeInfoDb")
+library("S4Vectors")
+library("GenomicAlignments")
+library("BSgenome.Hsapiens.UCSC.hg19")
+library("org.Hs.eg.db")
+library("BSgenome.Mmusculus.UCSC.mm10")
+library("org.Mm.eg.db")
+library("getopt")
+library("edgeR")
+# library("openxlsx")
+library("data.table")
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+source("https://bioconductor.org/biocLite.R")
+biocLite()
+source("https://bioconductor.org/biocLite.R")
+biocLite()
+library("getopt")
+library("edgeR")
+# library("openxlsx")
+library("data.table")
+source("https://bioconductor.org/biocLite.R")
+biocLite("edgeR")
+library("getopt")
+library("edgeR")
+# library("openxlsx")
+library("data.table")
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+# Get options using the spec as defined by the enclosed list
+# Options are read from the default: commandArgs(TRUE)
+option_specification = matrix(c(
+'input1', 'i1', 2, 'character',
+'input2', 'i2', 2, 'character',
+'input3', 'i3', 2, 'integer',
+'input4', 'i4', 2, 'integer',
+'output', 'o', 2, 'character'
+), byrow=TRUE, ncol=4);
+# Parse options
+options = getopt(option_specification)
+library("rworldmap")
+install.packages("rworldmap")
+library("rworldmap")
+theCountries <- c("DEU", "COD", "BFA")
+malDF <- data.frame(country = c("DEU", "COD", "BFA"),
+malaria = c(1, 1, 1))
+malMap <- joinCountryData2Map(malDF, joinCode = "ISO3",
+nameJoinColumn = "country")
+mapCountryData(malMap, nameColumnToPlot="malaria", catMethod = "categorical",
+missingCountryCol = gray(.8))
+require(rgdal)
+require(rgeos)
+require(ggplot2)
+install.packages("rgdal")
+install.packages("rgeos")
+require(rgdal)
+require(rgeos)
+require(ggplot2)
+655 + 290 + 658
+235+38+186
+370+357+50+37+59+386+30+112+300
+750+22+49+25+317
+750+22+49+25+317 +6
+239 + 61+760
+1060+1169+1701
+235+38+186
+3930+459
+653+571+546+211+
+0
+1981+1235+1148
+4364+43
+1701-40
+459+1661+1060
+459+1661+1060 +1169
+459-27
+370+205+6+179+360+455
+432+1575+1060+1169
+mat <- matrix(data = c(1:9), nrow = 3, ncol = 3, byrow = T)
+mat
+apply(mat, 1, mean)
+apply(mat, 2, mean)
+vec <- 1:10
+apply(X = vec, 1, print)
+apply(X = vec, 2, print)
+sapply(X = vec, FUN = print)
+sapply(X = vec, FUN = print, simplify = T)
+sapply(X = vec, FUN = print, simplify = F)
+sapply(X = vec, FUN = function(x) x -1)
+as.integer(c(4.1, 5.2, 6.3, 6.4))
+as.numeric(c(4.1, 5.2, 6.3, 6.4))
+?quantile
+?read.table
+?hist
+?boxplot
+?read.csv
+?quantile
+quantile(x <- rnorm(1001)) # Extremes & Quartiles by default
+res <- matrix(as.numeric(NA), 9, 7)
+res
+for(type in 1:9) res[type, ] <- y <- quantile(x,  p, type = type)
+dimnames(res) <- list(1:9, names(y))
+for(type in 1:9) res[type, ] <- y <- quantile(x,  p, type = type)
+setwd("~/Desktop/planemo_tools/16_fgsea")
+# Send R errors to stderr
+options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)})
+# Avoid crashing Galaxy with an UTF8 error on German LC settings
+loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
+# Import library
+library("getopt")
+library("fgsea")
+options(stringAsfactors = FALSE, useFancyQuotes = FALSE)
+# Take in trailing command line arguments
+args <- commandArgs(trailingOnly = TRUE)
+sessionInfo()