Calculate Position Weight Matrix (PWM) Scores for DNA Sequences

Usage

calc_seq_pwm(sequences, mdb, bidirect = TRUE)

Arguments

sequences: Character vector of DNA sequences.
mdb: MotifDB object containing PWMs.
bidirect: is the motif bi-directional. If TRUE, the reverse-complement of the motif will be used as well.

Value

A numeric matrix with sequences as rows and motifs as columns, containing PWM scores. Row names are preserved from input sequences if they exist. Column names are preserved from the PWM matrix if they exist.

Examples

sequences <- c("ACGTACGT", "TGCATGCA")
scores <- calc_seq_pwm(sequences, MOTIF_DB)