FindBestNormalParameters: FindBestNormalParameters takes takes a facets2n generated...

Description Usage Arguments Value

View source: R/facets-procreads.R

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

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FindBestNormalParameters(
  TumorLoess,
  TumorPileup,
  ReferenceLoess = NULL,
  ReferencePileup = NULL,
  MinOverlap = 0.9,
  useMatchedX = 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.

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 Feb. 6, 2020, 4:50 a.m.