BaalChIP.get: Method BaalChIP.get

In InesdeSantiago/align_parser: BaalChIP: Bayesian analysis of allele-specific transcription factor binding in cancer genomes

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]])

InesdeSantiago/align_parser documentation built on March 21, 2019, 12:06 a.m.