VanillaICE (version 1.34.0)

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

Description

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

Constructor for SnpArrayExperiment

Usage

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

data(snp_exp) # example

SnpArrayExperiment(cn=lrr(snp_exp), baf=baf(snp_exp),
                   rowRanges=rowRanges(snp_exp))