Motif: Motif objects

In motifRG: A package for discriminative motif discovery, designed for high throughput sequencing dataset

Description

A Motif object contains general motif characteristics and and details of motif match

Details

A motif object has the following slots: score:absolute z-value based on the logistic regression model for the motif. sign:the sign of the motif:plus for enriched motif in the foreground sequences, and negative for depleted motif count:a numeric vector holding the number of matches in each sequence match:a data.frame with the following columns: match.strand:the strand on which the match is found; pattern:the motif match pattern; seq.id: on which sequence the match is found; pos:the position relative to sequence start of the match. pattern:the motif pattern consensus:the motif consensus pattern determined by the majority votes at each position using the following rule: the most dominate single nucleotide if its frequency is greater than 0.6, or the two most dominate nucleotide if combined frequency is greater than 0.8, or the three most dominate nucleotide if combined frequency is greater than 0.95

See Also

findMotif summaryMotif plotMotif motifLatexTable

motifRG documentation built on April 28, 2020, 8:46 p.m.