counts2logROR: obtain logR and logOR from read counts and GC-correct logR

Description Usage Arguments

View source: R/facets-procreads.R

Description

obtain logR and logOR from read counts and GC-correct logR

Usage

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counts2logROR(
  mat,
  gbuild,
  unmatched = FALSE,
  MandUnormal = FALSE,
  f,
  spanT,
  spanA,
  spanX
)

Arguments

mat

input data

gbuild

e.g. "hg19"

unmatched

(logical)

MandUnormal

analyzing both matched and unmatched normal for log ratio normalization

f

default span value for loess

spanT

span value tumor

spanA

span value autosomes

spanX

span value X


rptashkin/facets2n documentation built on Feb. 6, 2020, 4:50 a.m.