get_samp_QC | R Documentation |
Perform QC step on single cells.
get_samp_QC(bambedObj)
bambedObj |
object returned from |
QCmetric |
A matrix containing total number/proportion of reads, total number/proportion of mapped reads, total number/proportion of mapped non-duplicate reads, and number/proportion of reads with mapping quality greater than 20 |
Rujin Wang rujin@email.unc.edu
library(WGSmapp) library(BSgenome.Hsapiens.UCSC.hg38) bamfolder <- system.file('extdata', package = 'WGSmapp') bamFile <- list.files(bamfolder, pattern = '*.dedup.bam$') bamdir <- file.path(bamfolder, bamFile) sampname_raw <- sapply(strsplit(bamFile, '.', fixed = TRUE), '[', 1) bambedObj <- get_bam_bed(bamdir = bamdir, sampname = sampname_raw, hgref = "hg38") QCmetric_raw = get_samp_QC(bambedObj)
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