BaalChIP.report: Method BaalChIP.report

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

Description

Method BaalChIP.report

Generates a data.frame per group with all variants and a label for all identified allele-specific binding (ASB) variants.

Usage

BaalChIP.report(.Object)

## S4 method for signature 'BaalChIP'
BaalChIP.report(.Object)

Arguments

.Object

An object of the BaalChIP class.

Details

The reported data frame contains the following columns:

• ID: unique identifier string per analysed variant.

• CHROM: chromosome identifier from the reference genome per variant.

• POS: the reference position (1-based).

• REF: reference base. Each base must be one of A,C,G,T in uppercase.

• ALT: alternate non-reference base. Each base must be one of A,C,G,T in uppercase.

• REF.counts: pooled counts of all reads with the reference allele.

• ALT.counts: pooled counts of all reads with the non-reference allele.

• Total.counts: pooled counts of all reads (REF + ALT).

• AR: allelic ratio calculated directly from sequencing reads (REF / TOTAL).

• RMbias: numerical value indicating the value estimated and applied by BaalChIP for the reference mapping bias. A value between 0.5 and 1 denotes a bias to the reference allele, and a value between 0 and 0.5 a bias to the alternative allele.

• RAF: numerical value indicating the value applied by BaalChIP for the relative allele frequency (RAF) bias correction. A value between 0.5 and 1 denotes a bias to the reference allele, and a value between 0 and 0.5 a bias to the alternative allele.

• Bayes_lower: lower interval for the estimated allelic ratio (allelic ratio is given by REF / TOTAL).

• Bayes_upper: upper interval for the estimated allelic ratio (allelic ratio is given by REF / TOTAL).

• Corrected.AR: average estimated allelic ratio (average between Bayes_lower and Bayes_upper). A value between 0.5 and 1 denotes a bias to the reference allele, and a value between 0 and 0.5 a bias to the alternative allele.

• isASB: logical value indicating BaalChIP's classification of variants into allele-specific.

Value

A named list, with a data.frame per group.

Author(s)

Ines de Santiago

See Also

summaryASB, getASB

Examples

data('BaalObject')
report <- BaalChIP.report(BaalObject)

#the reported list is grouped by group_name:
names(report)

#check out the report for one of the groups:
head(report[['MCF7']])

BaalChIP documentation built on Nov. 8, 2020, 5:23 p.m.