BaalChIP.report {BaalChIP} | R Documentation

## Method BaalChIP.report

### 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']])

[Package BaalChIP version 1.12.0 Index]