#!/usr/bin/env Rscript
options(echo=TRUE)
#devtools::install_github("homonecloco/bio.tilling")
require('bio.tilling')
args <- commandArgs(trailingOnly = TRUE)
filename<-args[1]
geneticMapFile<-args[2]
cores<-as.integer(args[3])
geneticMap<-read.csv(geneticMapFile, header=T)
covs<-readCoverageTable(filename)
covs<-filterSamplesPerSD(covs, maxSD=0.3)
df<-getExonsDF(covs)
mat<-normalizeCovs(covs, df)
rm(covs)
mat<-filterLowQualityExons(mat, maxSD=0.3)
df<-getExonsDF(mat)
dels<-getAllDeletedExons(mat,df)
libSD<-getLibSD(mat)
scaffsWithDels<-getAllScaffoldsWithDeletions(df,dels)
deslWithAVGs<-getAllScaffoldAveragesParallel(scaffsWithDels, mat,df, cores=cores)
selectedDels<-deslWithAVGs[deslWithAVGs$Score>=1,]
write.csv(dels, file="dels.csv")
write.csv(deslWithAVGs, file='deslWithAVGs.csv')
write.csv(df, file='df.csv')
write.csv(geneticMap, file='geneticMap.csv')
write.csv(libSD, file='libSD.csv')
write.csv(mat, file='mat.csv')
write.csv(scaffsWithDels, file='scaffsWithDels.csv')
write.csv(selectedDels, file='selectedDels.csv')
#tableWithAllDels <- getDeletionsPerCM(geneticMap,selectedDels, mat)
#write.csv(tableWithAllDels, file='tableWithAllDels.csv')
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