Generate gap imputed coverage from fragCounter output

Given fragCounter coverage with small, zero signal gaps, run neighbrohood-based partition regression gap imputation in a parallel manner to produce a gap imputed coverage file that is provides cleaner foreground signal in JaBbA and GISTIC.

Usage

get_cov_gap_imputation(
  path_to_fragcounter_cov,
  cpus = 1,
  make_diagnostic_plots = FALSE,
  path_to_diagnostic_plots_dir = NULL,
  exp_colnames = c("reads", "gc", "map", "reads.corrected"),
  verbose = T
)

Arguments

path_to_fragcounter_cov

Path to fragCounter coverage RDS

cpus

Number of CPUs to use for parallel execution, default: 1

make_diagnostic_plots

Generate diagnostic plots for each imputed gap, default: FALSE

path_to_diagnostic_plots_dir

Path to directory to place diagnostic plot PNGs

exp_colnames

Expected column names for coverage input GR

verbose

Output CLI during workflow, default: TRUE

Value

GenomicRanges object with gap imputed coverage