SnpArrayExperiment-class {VanillaICE}R Documentation

A RangedSummarizedExperiment-derived class of marker-level SNP array data for copy number inference

Description

Constructor for SnpArrayExperiment

Usage

SnpArrayExperiment(
  cn,
  baf,
  rowRanges = GRanges(),
  colData = DataFrame(),
  isSnp = logical(),
  ...
)

## S4 method for signature 'missing'
SnpArrayExperiment(
  cn,
  baf,
  rowRanges = GRanges(),
  colData = DataFrame(),
  isSnp = logical(),
  ...
)

## S4 method for signature 'matrix'
SnpArrayExperiment(
  cn,
  baf,
  rowRanges = GRanges(),
  colData = DataFrame(row.names = colnames(cn)),
  isSnp = logical(),
  ...
)

Arguments

cn

matrix of copy number estimates (e.g., log R ratios)

baf

matrix of B allele frequencies

rowRanges

GRanges object for SNPs/nonpolymorphic markers

colData

DataFrame containing sample-level covariates

isSnp

logical vector indicating whether marker is a SNP

...

additional arguments passed to SummarizedExperiment() constructor function

Examples

## empty container
library(VanillaICE)
data(snp_exp, package="VanillaICE") # example

se <- SnpArrayExperiment(cn=lrr(snp_exp), baf=baf(snp_exp),
                   rowRanges=rowRanges(snp_exp))

[Package VanillaICE version 1.50.0 Index]