#!/usr/bin/env Rscript
# pipeline
# go from aligned bam files to log fold change counts
#' Compute log fold change from bam files
#'
#' Output of this function is also stored in data/hisat2.er.rda
#'
#' @param project
#' @param aligner
#' @param experiment_definitions
#' @param base_input_dir
#' @return nothing. writes output to file
#' @export
step_010_lfc <- function(project, aligner, experiment_definitions, base_input_dir, lfc_dir) {
print("010_lfc")
# set up the input/output locations
# loading bam.files
filenames <- as.character(experiment_definitions$Bam.File)
filenames <- paste(base_input_dir, filenames, sep="/")
if (all(file.exists(filenames))) {
bamfiles <- Rsamtools::BamFileList(filenames)
seqinfo(bamfiles[1])
# counting reads
ER_lfc <- Rsubread::featureCounts(filenames,annot.inbuilt="hg38",isPairedEnd=TRUE)
# store data if we have regenerated it
#usethis::use_data(ER_lfc) # store in package
saveRDS(ER_lfc, file.path(lfc_dir, paste(aligner, project, "Rds", sep=".")))
}
else {
print("using cached file. To run these steps, Download BAM files from ... and put in the dir specified by base_input_dir")
# else get data from pregenerated data
data(ER_lfc, package="NEMpipeline")
# and save to local data
saveRDS(ER_lfc, file.path(lfc_dir, paste(aligner, project, "Rds", sep=".")))
}
}
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