Table of allele counts etc. from a DNAse-seq dataset.
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A data frame with 28942 rows and 12 variables:
chromosome
genomic location based on hg19
total number of reads covering the SNP
total number of reads at the SNP from the maternal allele
the allele with more ChIP-seq reads. "P" if xm < m/2 and "M" otherwise
the ID and the transcription factor name of the motif in JASPAR database (Mathelier and others, 2013).
the p-value of the motif on the maternal allele from R package
atSNP
the allele with stronger motif, e.g. it is "M" if pval.mat.atSNP < pval.pat.atSNP
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.
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.
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