FindBestNormalParameters: FindBestNormalParameters takes takes a facets2n generated...

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

FindBestNormalParameters takes takes a facets2n generated tumor loess object and snp-pileup generated pileup file, and optional similar files for reference normals, and returns the pileup data for the best normal for T/N CNLR.

Description

FindBestNormalParameters takes takes a facets2n generated tumor loess object and snp-pileup generated pileup file, and optional similar files for reference normals, and returns the pileup data for the best normal for T/N CNLR.

Usage

FindBestNormalParameters(
  TumorLoess,
  TumorPileup,
  ReferenceLoess = NULL,
  ReferencePileup = NULL,
  MinOverlap = 0.9,
  useMatchedX = FALSE,
  refX = FALSE,
  unmatched = FALSE
)

Arguments

TumorLoess	(matrix) A facets2n generated TumorLoess matrix with header and span values in the first row.
TumorPileup	(data frame) snp-pileup generated pileup data frame with sample columns that match with the TumorLoess object.
ReferenceLoess	(matrix) A ReferenceLoess matrix with a header and span values in the first row.
ReferencePileup	(data frame) A snp-pileup generated pileup data frame with sample columns that match with the ReferenceLoess object.
MinOverlap	(numeric) A numeric between 0 and 1 that denotes the fraction overlap of loci between TumorLoess and the optional ReferenceLoess
useMatchedX	(logical) Force select matched normal for normalization in ChrX.
refX	(logical) Use matched or reference normal for chrX normalization. excludes unmatched normals, such as pooled references, present in tumor counts matrix.
unmatched	(logical)

Value

A list of data frame with pileup depth values of Tumor, matched Normal, and a best unmatched normal, and the associated span values.

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