getCellDPTrack: getCellDPTrack Generates the DataTrack for plotting DP of a...

In ruqianl/comapr: Crossover analysis and genetic map construction

getCellDPTrack Generates the DataTrack for plotting DP of a selected cell

Description

It plots the total allele counts for the selected cell.

Usage

getCellDPTrack(
  chrom = "chr1",
  path_loc = "./output/firstBatch/WC_522/",
  sampleName = "WC_522",
  nwindow = 80,
  barcodeFile,
  cellBarcode,
  snp_track = NULL,
  chunk = 1000L,
  log = TRUE,
  plot_type = "hist"
)

Arguments

chrom,	the chromosome
path_loc,	the path prefix to the output files from sscocaller including "*_totalCount.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
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,	A integer scalar indicating the chunk size to use, i.e., number of rows to read at any one time.
log	whether the histogram of SNP density should be plotted on log scale (log10)
plot_type	the DataTrack plot type, default to be 'hist'

Value

The DataTrack object defined in DataTrack

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)
dp_co_tracks <- getCellDPTrack(chrom ="chr1",
                               path_loc = demo_path,
                               sampleName = "s1",
                               barcodeFile = file.path(demo_path,
                                                    "s1_barcodes.txt"),
                               cellBarcode = "BC1")

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