MotifSearchResult-class

This document described the MotifSearchResult class and methods for storing results from motif finding methods (e.g. MEME, FIMO and MAST).

# S4 method for MotifSearchResult
show(object)

# S4 method for MotifSearchResult,ANY
[(x, i, j, ..., drop = FALSE)

nmotif(object)

nseq(object)

motifNames(object)

sequenceNames(object)

scores(object)

pwm(object)

Arguments

object

MotifSearchResult object.
x

MotifSearchResult object.
i

row number (motif).
j

column number (sequence).
...

further arguments passed down to method.
drop

logical; whether to coerce to vector when number of columns equal one.

Slots

info

list with result information.

sequences

AnnotatedDataFrame with sequence information.

motifs

AnnotatedDataFrame with motif information.

probabilities

list of motif probabilities.

scores

list of motif scores.

ranges

GRanges with motif hits.