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 1.52.0 Index]