perCellChrQC: perCellChrQC

In ruqianl/comapr: Crossover analysis and genetic map construction

perCellChrQC

Description

A function that parses output ('_viSegInfo.txt' )from 'sgcocaller' https://gitlab.svi.edu.au/biocellgen-public/sgcocaller and generate cell cell (per chr) summary statistics

Usage

perCellChrQC(
  sampleName,
  chroms = c("chr1", "chr7", "chr15"),
  path,
  barcodeFile = NULL,
  doPlot = TRUE
)

Arguments

sampleName,	the name of the sample to parse which is used as prefix for finding relevant files for the underlying sample
chroms,	the character vectors of chromosomes to parse. Multiple chromosomes' results will be concated together.
path,	the path to the files, with name patterns *chrom_vi.mtx, *chrom_viSegInfo.txt, end with slash
barcodeFile,	defaults to NULL, it is assumed to be in the same d irectory as the other files and with name sampleName_barcodes.txt
doPlot,	whether a plot should returned, default to TRUE

Value

a list object that contains the data.frame with summarised statistics per chr per cell and a plot (if doPlot)

Author(s)

Ruqian Lyu

Examples

demo_path <-system.file("extdata",package = "comapr")
pcQC <- perCellChrQC(sampleName="s1",chroms=c("chr1"),
path=demo_path,
barcodeFile=NULL)

ruqianl/comapr documentation built on Oct. 27, 2023, 5:12 a.m.