perSegChrQC: perSegChrQC

In ruqianl/comapr: Crossover analysis and genetic map construction

perSegChrQC

Description

Plots the summary statistics of segments that are generated by 'sgcocaller' https://gitlab.svi.edu.au/biocellgen-public/sgcocaller which have been detected by finding consequtive viter states along the list of SNP markers.

Usage

perSegChrQC(
  sampleName,
  chroms = c("chr1", "chr7", "chr15"),
  path,
  barcodeFile = NULL,
  maxRawCO = 10
)

Arguments

sampleName,	the name of the sample to parse which is used as prefix for finding relevant files for the underlying sample
chroms,	the vector of chromosomes
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 directory as the other files and with name sampleName_barcodes.txt
maxRawCO,	if a cell has more than 'maxRawCO' number of raw crossovers called across a chromosome, the cell is filtered out#'

Details

It provides guidance in filtering out close double crossovers that are not likely biological but due to technical reasons as well as crossovers that are supported by fewer number of SNPs at the ends of the chromosomes.

Value

Histogram plots for statistics summarized across all Viterbi state segments

Author(s)

Ruqian Lyu

Examples

demo_path <- system.file("extdata",package = "comapr")
s1_rse_qc <- perSegChrQC(sampleName="s1",
                            chroms=c("chr1"),
                            path=demo_path, maxRawCO=10)

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