Count the number of motifs in a set of sequences and generate a motif count matrix

Detect all matches of a given motif (typically a short string) in a (typically long sequence) reference sequence or set of reference sequences. For each sequence and each motif a count matrix is generated and returned.

motif_count_matrix(file, motifs, max.mismatch = 0, min.mismatch = 0, ...)

Arguments

file

a file path to the fasta file storing the sequences of interest.

motifs

a character string specifying the sequence motifs that shall be screened and counted.

max.mismatch

the maximum number of mismatching letters allowed (see matchPattern for details).

min.mismatch

the minimum number of mismatching letters allowed (see vcountPattern for details).

...

additional arguments passed to matchPattern.

Author

Hajk-Georg Drost