BaalChIP.report {BaalChIP} | R Documentation |
Method BaalChIP.report
Generates a data.frame per group with all variants and a label for all identified allele-specific binding (ASB) variants.
BaalChIP.report(.Object) ## S4 method for signature 'BaalChIP' BaalChIP.report(.Object)
.Object |
An object of the |
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.
A named list, with a data.frame per group.
Ines de Santiago
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']])