perform_qc: Quality control for cells and bins

In rujinwang/SCOPE: A normalization and copy number estimation method for single-cell DNA sequencing

Quality control for cells and bins

Description

Perform QC step on single cells and bins.

Usage

perform_qc(Y_raw, sampname_raw, ref_raw, QCmetric_raw,
        cov_thresh = 0, minCountQC = 20, 
        mapq20_thresh = 0.3, mapp_thresh = 0.9,
        gc_thresh = c(20, 80), nMAD = 3)

Arguments

Y_raw	raw read count matrix returned from get_coverage_scDNA
sampname_raw	sample names for quality control returned from get_bam_bed
ref_raw	raw GRanges object with corresponding GC content and mappability for quality control returned from get_bam_bed
QCmetric_raw	a QC metric for single cells returned from get_samp_QC
cov_thresh	scalar variable specifying the lower bound of read count summation of each cell. Default is 0
minCountQC	the minimum read coverage required for normalization and EM fitting. Defalut is 20
mapq20_thresh	scalar variable specifying the lower threshold of proportion of reads with mapping quality greater than 20. Default is 0.3
mapp_thresh	scalar variable specifying mappability of each genomic bin. Default is 0.9
gc_thresh	vector specifying the lower and upper bound of GC content threshold for quality control. Default is 20-80
nMAD	scalar variable specifying the number of MAD from the median of total read counts adjusted by library size for each cell. Default is 3

Value

A list with components

Y	read depth matrix after quality control
sampname	sample names after quality control
ref	A GRanges object specifying whole genomic bin positions after quality control
QCmetric	A data frame of QC metric for single cells after quality control

Author(s)

Rujin Wang [e-mail]

Examples

Y_raw <- coverageObj.scopeDemo$Y
sampname_raw <- rownames(QCmetric.scopeDemo)
ref_raw <- ref.scopeDemo
QCmetric_raw <- QCmetric.scopeDemo
qcObj <- perform_qc(Y_raw = Y_raw, sampname_raw = sampname_raw,
                ref_raw = ref_raw, QCmetric_raw = QCmetric_raw)

rujinwang/SCOPE documentation built on Jan. 1, 2023, 5:40 a.m.