readHapState: readHapState

In ruqianl/comapr: Crossover analysis and genetic map construction

readHapState

Description

A function that parses the viterbi state matrix (in .mtx format), barcode.txt and snpAnno.txt files for each individual.

Usage

readHapState(
  sampleName,
  chroms = c("chr1"),
  path,
  barcodeFile = NULL,
  minSNP = 30,
  minlogllRatio = 200,
  bpDist = 100,
  maxRawCO = 10,
  nmad = 1.5,
  minCellSNP = 200,
  biasTol = 0.45
)

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,	if NULL, it is assumed to be in the same directory as the other files and with name sampleName_barcodes.txt
minSNP	the crossover(s) will be filtered out if introduced by a segment that has fewer than 'minSNP' SNPs to support.
minlogllRatio	the crossover(s) will be filtered out if introduced by a segment that has lower than 'minlogllRatio' to its reversed state.
bpDist,	the crossover(s) will be filtered out if introduced by a segment that is shorter than 'bpDist' basepairs. It can be a single value or a vector that is the same length and order with 'chroms'.
maxRawCO	if a cell has more than 'maxRawCO' number of raw crossovers called across a chromosome, the cell is filtered out
nmad	how many mean absolute deviations lower than the median number of SNPs per cellfor a cell to be considered as low coverage cell and filtered Only effective when number of cells are larger than 10. When effective, this or 'minCellSNP', whichever is larger, is applied
minCellSNP	the minimum number of SNPs detected for a cell to be kept, used with 'nmads'
biasTol	the SNP's haplotype ratio across all cells is assumed to be 1:1. This argument can be used for removing SNPs that have a biased haplotype. i.e. almost always inferred to be haplotype state 1. It specifies a bias tolerance value, SNPs with haplotype ratios deviating from 0.5 smaller than this value are kept. Only effective when number of cells are larger than 10

Value

a RangedSummarizedExperiment with rowRanges as SNP positions that contribute to crossovers in any cells. colData contains cells annotation including barcodes and sampleName.

Author(s)

Ruqian Lyu

Examples

demo_path <- system.file("extdata",package = "comapr")
s1_rse_state <- readHapState(sampleName="s1",chroms=c("chr1"),
path=paste0(demo_path,"/"),
barcodeFile=NULL,minSNP = 0, minlogllRatio = 50,
bpDist = 100,maxRawCO=10,minCellSNP=3)
s1_rse_state

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