getCellAFTrack: getCellAFTrack Generates the DataTracks for plotting AF and...

In ruqianl/comapr: Crossover analysis and genetic map construction

getCellAFTrack Generates the DataTracks for plotting AF and crossover regions

Description

It plots the raw alternative allele frequencies and highlight the crossover regions for the selected cell.

It plots the raw alternative allele frequencies and highlight the crossover regions for the selected cell.

Usage

getCellAFTrack(
  chrom = "chr1",
  path_loc = "./output/firstBatch/WC_522/",
  sampleName = "WC_522",
  nwindow = 80,
  barcodeFile,
  cellBarcode,
  co_count,
  snp_track = NULL,
  chunk = 1000L
)

getCellAFTrack(
  chrom = "chr1",
  path_loc = "./output/firstBatch/WC_522/",
  sampleName = "WC_522",
  nwindow = 80,
  barcodeFile,
  cellBarcode,
  co_count,
  snp_track = NULL,
  chunk = 1000L
)

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
cellBarcode,	the selected cell barcode
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.
chunk,	An integer scalar indicating the chunk size to use, i.e., number of rows to read at any one time.

Value

The DataTrack object defined in DataTrack

The DataTrack object defined in DataTrack

Author(s)

Ruqian Lyu

Examples

demo_path <-paste0(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 <- getCellAFTrack(chrom ="chr1",
                               path_loc = demo_path,
                               sampleName = "s1",
                               barcodeFile = paste0(demo_path,
                                                    "s1_barcodes.txt"),
                               cellBarcode = "BC1",
                               co_count = s1_counts)

demo_path <-paste0(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 <- getCellAFTrack(chrom ="chr1",
                               path_loc = demo_path,
                               sampleName = "s1",
                               barcodeFile = paste0(demo_path,
                                                    "s1_barcodes.txt"),
                               cellBarcode = "BC1",
                               co_count = s1_counts)

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