prep_scrnaseq: Quality control of scRNAseq

In rosedu1/deconvSeq: Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing

Description

do quality control of scRNAseq based on library size, feature counts, chrM, cell cycle phase, and count threshold

Usage

prep_scrnaseq(
  scrna_mat,
  genenametype = "hgnc_symbol",
  cellcycle = NULL,
  count.threshold = NULL
)

Arguments

scrna_mat	count matrix for single cell RNAseq
genenametype	nomenclature for genes in count matrix: "hgnc_symbol" or "ensembl_id". Default is "hgnc_symbol".
cellcycle	filter for specific cell cycle phase: "G1", "G2M", or "S". Default is NULL, for no cell cycle phase filtering.
count.threshold	remove genes where average count is less than count.threshold. Default is NULL, for no count threshold filtering

Value

count matrix after quality control

Examples

## Not run: 
data("data_scrnaseq") 
cnts.sc = prep_scrnaseq(cnts.scrnaseq,cellcycle=NULL,count.threshold=0.05)

## End(Not run)

rosedu1/deconvSeq documentation built on Aug. 19, 2020, 7:10 p.m.