atac: Table of allele counts etc. from an ATAC-seq dataset.
In anthony-aylward/npbin:

Table of allele counts etc. from an ATAC-seq dataset.

atac

A data frame with 39659 rows and 12 variables:

chr: chromosome
location: genomic location based on hg19
m: total number of reads covering the SNP
xm: total number of reads at the SNP from the maternal allele
winning.chip: the allele with more ChIP-seq reads. "P" if xm < m/2 and "M" otherwise
motif: the ID and the transcription factor name of the motif in JASPAR database (Mathelier and others, 2013).
pval.mat.atSNP: the p-value of the motif on the maternal allele from R package atSNP
winning.motif: the allele with stronger motif, e.g. it is "M" if pval.mat.atSNP < pval.pat.atSNP
potential.TP: whether it is a potential TP based on our criteria described in the Supplementary notes. The users can define it differently using different thresholds on the various p-values from atSNP.
potential.FP: whether it is a potential FP based on our criteria described in the Supplementary notes. The users can define it differently using different thresholds on the various p-values from atSNP.