segmentRawData: This function runs the copynumber::pcf algorithm to segment...

In gerstung-lab/BarrettsProgressionRisk: Prognositc adenocarcinoma risk prediction for Barrett's Esophagus

Description

This function runs the copynumber::pcf algorithm to segment the sWGS data. renamed from 'binSWGS'

Usage

segmentRawData(info, raw.data, fit.data,
  blacklist = readr::read_tsv(system.file("extdata",
  "qDNAseq_blacklistedRegions.txt", package = "BarrettsProgressionRisk"),
  col_names = T, col_types = "cii"), gamma2 = 250, kb = 50,
  cutoff = 0.008, multipcf = T, logTransform = F,
  cache.dir = getcachedir(), build = "hg19", verbose = T)

Arguments

raw.data	Data frame of raw read counts (file name is also valid)
fit.data	Data frame of fitted read values (file name is also valid)
blacklist	qDNAseq_blacklistedRegions (defaults to file provided in package)
gamma2	gamma adjustment for pcf DEF=250
kb	QDNAseq bin size
cutoff	is the residual value cutoff for QC DEF=0.015
logTransform	DEF=F
norm	normalize pcf, DEF=T

Value

list of objects: 'seg.vals'=segmented samples that have passed QC, 'residuals'=data frame of per-sample residuals, 'prepped.data'=adjusted raw values, 'seg.plots'=list of per-sample genome-wide plots, 'genome.coverage'=calculated genome coverage, 'failedQC'=segmented samples that have failed QC

Author(s)

skillcoyne

gerstung-lab/BarrettsProgressionRisk documentation built on June 22, 2021, 3:12 p.m.