preprocess_cov_for_dryclean: preprocess_cov_for_dryclean

In mskilab/skitools: Various mskilab R utilties

preprocess_cov_for_dryclean

Description

preprocess coverage file by rebinning to match the ranges that are compatible with the PON and by normalizing the coverage by the mean

Usage

preprocess_cov_for_dryclean(
  cov,
  field = "reads.corrected",
  template_rds = "",
  seqnames.to.include = c(as.character(1:22), "X"),
  output.field = "reads.corrected",
 
    pon_dict = "/gpfs/commons/groups/imielinski_lab/DB/modules/dryclean/dryclean_pon_dictionary.tsv",
  pon_name = NULL,
  nochr = TRUE
)

Arguments

cov	GRanges with coverage data
field	field to use as input from the coverage GRanges
template_rds	path to a RDS file containing the template GRanges to use for re-binning
seqnames.to.include	which seqnames to include in the output
output.field	field name for the output normalized and rebinned data
pon_dict	path to the TAB delimited file PON dictionary (if no template_rds was provided then you must provide a pon_name)
pon_name	name of the PON. This is used to get the path to the template RDS from the pon_dict (if no template_rds was provided then you must provide a pon_name)
nochr	by default all chr prefix is removed, if you wish the output to have chr you must specify nochr=FALSE

Value

new.cov GRanges object with the normalized and rebinned coverage values

Author(s)

Alon Shaiber

mskilab/skitools documentation built on Aug. 31, 2023, 1:13 p.m.