comparison region_motif_compare.r @ 31:0e031bf8c5b1 draft

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30:da0bc6dead0d

# Description: Reads in two count files and determines enriched and depleted
# motifs (or any location based feature) based on poisson tests and gc
# corrections. All enrichment ratios relative to overall count / gc ratios.
# Author: Jeremy liu
# Email: [e-mail]
# Date: 14/07/03
# Note: This script is meant to be invoked with the following command
# R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <db> <intab1> <intab2> 
#   <enriched_tab> <depleted_tab> <plots_png>
# <workingdir> is working directory of galaxy installation
# <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse, "c" combined

options(warn=-1)

# Set common and data directories
args <- commandArgs()
workingDir = args[7]
dbDir = concat(workingDir, "/region_motif_db")
dbCode = args[8]
# dbCode "c" implemented when pwmFile is loaded
if (dbCode == "t" | dbCode == "p") {
	pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData")
} else if (dbCode == "j") {
	pwmFile = concat(dbDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
} else if (dbCode == "m") {
	pwmFile = concat(dbDir, "/pwms/mm9.pwms.from.seq.RData")
} else if (dbCode == "c") { # rest of dbCode "c" implemeted when pwmFile loaded
	pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData")
	pwmFile2 = concat(dbDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
} else {
	pwmFile = concat(dbDir, "/pwms/pouya.pwms.from.seq.RData")
}

# Set input and reference files
inTab1 = args[9]
inTab2 = args[10]
enrichTab = args[11]
depleteTab = args[12]
plotsPng = args[13]

# Load dependencies
source(concat(workingDir, "/region_motif_lib/plotting.r"))

# Auxiliary function to read in tab file and prepare the data
read_tsv <- function(file) {
	data = read.table(file, sep="\t", stringsAsFactors=FALSE)
	names(data)[names(data) == "V1"] = "motif"

31:0e031bf8c5b1

# Description: Reads in two count files and determines enriched and depleted
# motifs (or any location based feature) based on poisson tests and gc
# corrections. All enrichment ratios relative to overall count / gc ratios.
# Author: Jeremy liu
# Email: [e-mail]
# Date: 15/02/04
# Note: This script is meant to be invoked with the following command
# R --slave --vanilla -f ./region_motif_compare.r --args <workingdir> <db> <intab1> <intab2> 
#   <enriched_tab> <depleted_tab> <plots_png>
# <workingdir> is working directory of galaxy installation
# <db> types: "t" test, "p" pouya, "j" jaspar jolma, "m" mouse, "c" combined

options(warn=-1)

# Set common and data directories
args <- commandArgs()
workingDir = args[7]
dbCode = args[8]
# dbCode "c" implemented when pwmFile is loaded
if (dbCode == "t" | dbCode == "p") {
	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
} else if (dbCode == "j") {
	pwmFile = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
} else if (dbCode == "m") {
	pwmFile = concat(workingDir, "/pwms/mm9.pwms.from.seq.RData")
} else if (dbCode == "c") { # rest of dbCode "c" implemeted when pwmFile loaded
	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
	pwmFile2 = concat(workingDir, "/pwms/jaspar.jolma.pwms.from.seq.RData")
} else {
	pwmFile = concat(workingDir, "/pwms/pouya.pwms.from.seq.RData")
}

# Set input and reference files
inTab1 = args[9]
inTab2 = args[10]
enrichTab = args[11]
depleteTab = args[12]
plotsPng = args[13]

# Load dependencies
source(concat(workingDir, "/plotting.r"))

# Auxiliary function to read in tab file and prepare the data
read_tsv <- function(file) {
	data = read.table(file, sep="\t", stringsAsFactors=FALSE)
	names(data)[names(data) == "V1"] = "motif"