getSNPDensityTrack: getSNPDensityTrack

In ruqianl/comapr: Crossover analysis and genetic map construction

getSNPDensityTrack

Description

Generate the SNP density DataTrack (from 'Gviz') for selected chromosome

Usage

getSNPDensityTrack(
  chrom = "chr1",
  sampleName = "s1",
  path_loc = ".",
  nwindow = 80,
  plot_type = "hist",
  log = TRUE
)

Arguments

chrom	the chromosome
sampleName	the sample name, which is the prefix of sscocaller's output files
path_loc	the path prefix to the output files from sscocaller including "*_totalCount.mtx" and "_altCount.mtx"
nwindow	the number of windows for binning the chromosome
plot_type,	the DataTrack plot type, default to be 'hist'
log,	whether the histogram of SNP density should be plotted on log scale (log10)

Value

DataTrack object plotting the SNP density histogram

Author(s)

Ruqian Lyu

Examples

demo_path <- system.file("extdata",package = "comapr")
snp_track <- getSNPDensityTrack(chrom ="chr1",
                               path_loc = demo_path,
                               sampleName = "s1")

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