summaryMotif: summarize a list of motifs

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

Description

Create a summary table of a list of motifs found by findMotif

Usage

summaryMotif(motifs, category)

Arguments

motifs	a list of motifs of class Motif-class
category	a vector of 0 or 1, specifying which sequences are foreground and background. Input for findMotif

Value

A data.frame with following columns:

scores	scores for each Motif. All values are negative. The absolute scales of the scores reflect the discriminative power of the motif for separating the foreground and background. Statistically, they correspond to the Z-values of the predictor(counts of the motifs in this case) in the logistic regression model
signs	sign of the motifs. TRUE for enriched motifs, FALSE for depleted motifs
fg.hits, bg.hits	Total number of hits in the foreground, and background sequences. If the motif is scanned on both strands of the input sequences, the counts on both strands are added.
fg.seq, bg.seq	The number of sequences that contain at least one motif match in the foreground, and the background

.

ratio	The enrichment/depleted ratio of motifs
fg.frac,bg.frac	The fraction of foreground/background sequences that contain at least one motif match

See Also

findMotif motifLatexTable motifHtmlTable

Examples

data(ctcf.motifs)
###plot the summary statics of motif matches after masking previous motif ocurrences###
summaryMotif(ctcf.motifs$mask.motifs, ctcf.motifs$category)

###plot the summary statics of motif matches in the original sequences###
summaryMotif(ctcf.motifs$motifs, ctcf.motifs$category)

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