#!/usr/bin/env Rscript
library("optparse")
options(echo=TRUE)
require('bio.tilling')
option_list = list(
make_option(c("-f", "--coverage_file"),
type="character",
default=NULL,
help="Coverage file",
metavar="character"),
make_option(c("-s", "--sampleSD"),
type="double",
default=0.3,
help="Maximum Standard Deviation allowed in sample [default= %default]"),
make_option(c("-w", "--windowSD"),
type="double",
default=0.3,
help="Maximum Standard Deviation allowed in each window [default= %default]"),
make_option(c("-z", "--gzip"),
action="store_true",
default=FALSE,
help="The coverage file is gzipped [default]"),
make_option(c("-o", "--out"),
type="character",
default="./deletions_out",
help="output folder [default= %default]",
metavar="character")
);
opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);
opt
if (is.null(opt$coverage_file)){
print_help(opt_parser)
stop("At least one argument must be supplied (coverage_file).",
call.=FALSE)
}
filename<-unlist(opt$coverage_file)
output_folder<-opt$out
is_gz <- opt$gzip
covs<-readCoverageTable(filename, is_gz=is_gz)
covs<-filterSamplesPerSD(covs, maxSD=opt$sampleSD)
df<-getExonsDF(covs)
mat<-normalizeCovs(covs, df)
rm(covs)
dir.create(output_folder, recursive = TRUE)
setwd(output_folder)
mat<-filterLowQualityExons(mat, maxSD=opt$windowSD)
gc()
write.csv(mat, file='mat.csv')
df<-getExonsDF(mat)
write.csv(df, file='df.csv')
dels<-getAllDeletedExons(mat,df)
write.csv(dels, file="dels.csv")
libSD<-getLibSD(mat)
write.csv(libSD, file='libSD.csv')
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