countMatches: Obtain the number of sequences containing matches

In steveped/motifMatching: Functions used for matching motifs in DNA/RNA Strings

Description

Counts the number of XStringViews in a XStringSet which contain a match to a motif.

Usage

countViews(views, seqLength, singleHits = TRUE)

Arguments

views	contains the XStringViews which correspond to motif matches obtained previously
seqLength	the length of the sequences (i.e. promoters) initially searched
singleHits	logical. Determines whether a single match is returned for each sequence, regardless of multiple matches (singleHits=TRUE), or whether the number of total matches are returned (singleHits=FALSE)

Details

This function takes a set of XStringViews obtained by motif matching performed on an XStringSet which has been concatenated into a single XString. All strings in the original XStringSet must be the same length, which must be specified by the argument seqLength. This parameter cannot be calculated directly from the object supplied in views.

Value

The number of the initial sequences containing at least one match (singleHits = TRUE), or the total number of matches (singleHits = FALSE).

Author(s)

Steve Pederson

See Also

DNAStringSet

steveped/motifMatching documentation built on May 30, 2019, 5:39 p.m.