SnpArrayExperiment-class {VanillaICE} | R Documentation

## 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(), ...)

    ## 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
    SnpArrayExperiment()

    data(snp_exp) # example

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

[Package VanillaICE version 1.42.4 Index]