normCoverage: Coverage Normalization function

In kaistcbfg/covNormRpkg: an R package for coverage based normaliza-tion of Hi-C and capture Hi-C data

Description

Takes formatted dataframe and retunrs glm.nb fitted coeffs & normalized df

Usage

normCoverage(
  df,
  do_shuffle = TRUE,
  cov1_thresh = 200,
  cov2_thresh = 200,
  max_covnorm_value = 50,
  sample_ratio = -1
)

Arguments

df	An input dataframe.
max_covnorm_value	Outliers by division with too small a number are replaced by this value.
sample_ratio	If NOT -1 && between 0.0-1.0, downsample the df rows to be used for fitting by that ratio.
cov1_thresh&cov2_thresh	Threshold for filteraing bins with too low coverage.

Value

df Coverage normalized.

kaistcbfg/covNormRpkg documentation built on June 23, 2021, 12:55 p.m.