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comparison exomedepth.R @ 4:9ccde1867fbb draft

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Replaces Rscript by R CMD BATCH
author crs4
date Mon, 11 Jun 2018 09:32:44 -0400
parents 7697ae024df6
children 45af4a9748cf
comparison
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3:88b89f435f6a 4:9ccde1867fbb
1 # Load ExomeDepth library (without warnings) 1 # Load ExomeDepth library (without warnings)
2 suppressMessages(library(ExomeDepth)) 2 suppressMessages(library(ExomeDepth))
3 3
4 # Import parameters from xml wrapper (args_file) 4 # Import parameters from xml wrapper (args_file)
5 args <- commandArgs(trailingOnly=TRUE) 5 args <- commandArgs(trailingOnly=TRUE)
6 param <- read.table(args[1],sep="=", as.is=TRUE) 6 eval(parse(text=args[[1]]))
7 param <- read.table(mypars,sep="=", as.is=TRUE)
7 8
8 # Set common parameters 9 # Set common parameters
9 target <- param[match("target",param[,1]),2] 10 target <- param[match("target",param[,1]),2]
10 trans_prob <- as.numeric(param[match("trans_prob",param[,1]),2]) 11 trans_prob <- as.numeric(param[match("trans_prob",param[,1]),2])
11 output <- param[match("output",param[,1]),2] 12 output <- param[match("output",param[,1]),2]