Mercurial > repos > crs4 > exomedepth
comparison exomedepth.R @ 4:9ccde1867fbb draft
Replaces Rscript by R CMD BATCH
author | crs4 |
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date | Mon, 11 Jun 2018 09:32:44 -0400 |
parents | 7697ae024df6 |
children | 45af4a9748cf |
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3:88b89f435f6a | 4:9ccde1867fbb |
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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] |