BaalChIP.get {BaalChIP} | R Documentation |
Method BaalChIP.get
Get information from individual slots in a BaalChIP object.
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"))
.Object |
An object of the |
what |
a single character value specifying which information should be retrieved. Options: 'samples', 'param', 'alleleCountsPerBam', 'mergedCounts', 'assayedVar', 'biasTable'. |
The slot content from an object of the BaalChIP
class.
Ines de Santiago
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]])