FLCNA_QC: FLCNA_QC

In FeifeiXiaoUSC/FLCNA: Simultaneous CNV Detection And Subclone Clustering With Single Cell Sequencing Data

FLCNA_QC

Description

Perform QC step on single cells and bins.

Usage

FLCNA_QC(Y_raw, ref_raw, mapp_thresh = 0.9, gc_thresh = c(20, 80))

Arguments

Y_raw	raw read count matrix.
ref_raw	raw GRanges object with corresponding GC content and mappability for quality control.
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.

Value

A list with components after quality control.

Y	Read depth matrix after quality control.
ref	A GRanges object specifying whole genomic bin positions after quality control.

FeifeiXiaoUSC/FLCNA documentation built on March 29, 2025, 10:48 p.m.