BaalChIP.get {BaalChIP} | R Documentation

## Method BaalChIP.get

### Description

Method BaalChIP.get

Get information from individual slots in a BaalChIP object.

### Usage

    BaalChIP.get(.Object, what = c("samples", "param", "alleleCountsPerBam",
      "mergedCounts", "assayedVar", "biasTable"))

    ## S4 method for signature 'BaalChIP'
    BaalChIP.get(.Object, what = c("samples", "param",
      "alleleCountsPerBam", "mergedCounts", "assayedVar"))

### Arguments

`.Object` | An object of the `BaalChIP` class.
`what` | a single character value specifying which information should be retrieved. Options: 'samples', 'param', 'alleleCountsPerBam', 'mergedCounts', 'assayedVar', 'biasTable'.

### Value

The slot content from an object of the `BaalChIP` class.

### Author(s)

Ines de Santiago

### Examples

    data('BaalObject')

    #samples data spreadsheet and hets:
    BaalChIP.get(BaalObject,what='samples')

    #parameters used within run:
    BaalChIP.get(BaalObject,what='param')

    #retrieve a GRanges list with allele-specific read counts per BAM file:
    counts <- BaalChIP.get(BaalObject,what='alleleCountsPerBam')
    counts[['MCF7']][[1]]

    #retrieve a data.frame with allele-specific read counts per group:
    counts <- BaalChIP.get(BaalObject,what='mergedCounts')
    head(counts[[1]])

[Package BaalChIP version 1.12.0 Index]