example_run_calcRPKMsFromBAMs.R

# Install missing packages from CRAN
list.of.packages <- c("RCurl", "data.table", "parallel")
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)

# Install missing packages from Bioconductor
# Note: for Windows users: Rsubread has to be installed from file  
biocLitePackages <- c(GenomicRanges", "Rsubread","WES.1KG.WUGSC") 
new.biocLitePackage <- biocLitePackages[!(biocLitePackages %in% installed.packages()[,"Package"])]
if(length(new.biocLitePackage)) { source("http://bioconductor.org/biocLite.R"); biocLite(new.biocLitePackage)}

library(WES.1KG.WUGSC)
library(data.table)
library(parallel)
library(GenomicRanges)
library(Rsubread) 
library(RCurl)

mc.cores <- 8
dirPath <- system.file("extdata", package = "WES.1KG.WUGSC")
bamFile <- list.files(dirPath, pattern = '*.bam$')
bamdir <- file.path(dirPath, bamFile)
sampname <- as.matrix(read.table(file.path(dirPath, "sampname")))
bf <- file.path(dirPath, "chr22_400_to_500.bed")
tmpDir <- "~/tmp/"
outputRPKM <- "~/RPKMs/"
bedFile <- paste0(tmpDir,"chr22_400_to_500.bed")
dir.create(outputRPKM)
dir.create(tmpDir)
bed <- fread(bf)
bed$V1 <- paste0("chr", bed$V1)
bed$GeneName <- "dummy_gene"
write.table(bed, file=bedFile , sep="\t", quote=F, row.names=F, col.names=F)

# load HMZDelFinder source code
# Note: source ("https://....")  does not work on some platforms
eval( expr = parse( text = getURL("https://raw.githubusercontent.com/BCM-Lupskilab/HMZDelFinder/master/src/HMZDelFinder.R") ))
calcRPKMsFromBAMs  (bedFile, paste0(dirPath, "/", bamFile), sampname, outputRPKM, mc.cores)