summaryMotif: summarize a list of motifs

Description Usage Arguments Value See Also Examples

View source: R/motif.rg.R

Description

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

Usage

1

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

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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 May 2, 2018, 4:10 a.m.