library(argparse)
suppressPackageStartupMessages(library(epiRepeatR))
ap <- ArgumentParser()
ap$add_argument("-i", "--in", action="store", dest="input", help="Input file (bam)")
ap$add_argument("-j", "--chip", action="store", help="ChIP file (bam)")
ap$add_argument("-o", "--out", action="store", dest="output", help="Output file (rds)")
ap$add_argument("-c", "--config", action="store", help="Config file (json)")
ap$add_argument("-g", "--genome", action="store_true", dest="doGenomeAln", default=FALSE, help="Enables parsing from genome alignments.")
cmdArgs <- ap$parse_args()
logger.cmd.args(cmdArgs)
loadConfig(cmdArgs$config)
if (cmdArgs$doGenomeAln){
logger.info("Quantify enrichment from genome alignment")
ga.input <- readRDS(cmdArgs$input)
ga.chip <- readRDS(cmdArgs$chip)
quantObj <- epiRepeatR:::computeEnrichment(ga.chip, ga.input)
} else {
logger.info("Quantify enrichment from repeat alignment")
ra.input <- epiRepeatR:::RepeatAlignment(cmdArgs$input)
ra.chip <- epiRepeatR:::RepeatAlignmentChip(cmdArgs$chip)
quantObj <- epiRepeatR:::computeEnrichment(ra.chip, ra.input, useIdxStats=TRUE)
}
saveRDS(quantObj, cmdArgs$output)
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