getAFTracks: getAFTracks

In ruqianl/comapr: Crossover analysis and genetic map construction

getAFTracks

Description

Generate the raw alternative allele frequencies tracks for all cells in the columns of provided 'co_count'

Usage

getAFTracks(
  chrom = "chr1",
  path_loc = "./output/firstBatch/WC_522/",
  sampleName = "WC_522",
  nwindow = 80,
  barcodeFile,
  co_count,
  snp_track = NULL
)

Arguments

chrom	the chromosome
path_loc	the path prefix to the output files from sscocaller including "*_totalCount.mtx" and "_altCount.mtx"
sampleName	the sample name, which is the prefix of sscocaller's output files
nwindow	the number of windows for binning the chromosome
barcodeFile	the barcode file containing the list of cell barcodes used as the input file for sscocaller
co_count	'GRange' or 'RangedSummarizedExperiment' object, returned by countCO that contains the crossover intervals and the number of crossovers in each cell.
snp_track	the SNP position track which is used for obtaining the SNP chromosome locations. It could be omitted and the SNP positions will be acquired from the "*_snpAnnot.txt" file.

Value

a list object, in which each element is a list of two items with the cell's alternative allele frequency DataTrack and the called crossover ranges.

Author(s)

Ruqian Lyu

Examples

demo_path <- system.file("extdata",package = "comapr")
s1_rse_state <- readHapState("s1",chroms=c("chr1"),
                             path=demo_path,barcodeFile=NULL,minSNP = 0,
                             minlogllRatio = 50,
                             bpDist = 100,maxRawCO=10,
                             minCellSNP = 0)
s1_counts <- countCOs(s1_rse_state)

af_co_tracks <- getAFTracks(chrom ="chr1",
                               path_loc = demo_path,
                               sampleName = "s1",
                               barcodeFile = file.path(demo_path,
                                                    "s1_barcodes.txt"),
                               co_count = s1_counts)

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