MakeLoessObject: MakeLoessObject takes a pipleup file generated by snp-pileup...

In rptashkin/facets2n: Cellular Faction and Copy Numbers from Tumor Sequencing

MakeLoessObject takes a pipleup file generated by snp-pileup and generates a loess/lowess object, which is also optinally written into an output file.

Description

MakeLoessObject takes a pipleup file generated by snp-pileup and generates a loess/lowess object, which is also optinally written into an output file.

Usage

MakeLoessObject(
  pileup,
  write.loess = FALSE,
  outfilepath = "./loess.txt",
  is.Reference = FALSE,
  gbuild = "hg19"
)

Arguments

pileup	(data frame) A data franme of snp-pileup generated depth.
write.loess	(logical) Write loess object into file, instead of returning it as a matrix?
outfilepath	(character) Filepath for writing loess object.
is.Reference	(logical) Indicate whether the snp-pilep is Reference data.
gbuild	(character) genome build version.

Value

A dataframe of loess normalized values for all input samples against filtered loci or None, if the loess normalized value is to be written to an output file.

rptashkin/facets2n documentation built on May 11, 2022, 1:34 p.m.