BaalChIP.get {BaalChIP}

R Documentation

Method BaalChIP.get

Description

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]])

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