Count the matches to a PWM within an XStringSet — countPwmMatches • motifTestR

Count the matches to a PWM within an XStringSet

countPwmMatches(
  pwm,
  stringset,
  rc = TRUE,
  min_score = "80%",
  mc.cores = 1,
  ...
)

Arguments

pwm: A Position Weight Matrix
stringset: An XStringSet
rc: logical(1) Also find matches using the reverse complement of pwm
min_score: The minimum score to return a match
mc.cores: Passed to mclapply when analysing a list of PWMs
...: Passed to countPWM

Value

An integer vector

Details

Will simply count the matches within an XStringSet and return an integer. All matches are included.

Examples

## Load the example PWM
data("ex_pwm")
esr1 <- ex_pwm$ESR1

## Load the example Peaks
data("ar_er_seq")
countPwmMatches(esr1, ar_er_seq)
#> [1] 62

## Count all PWMs
countPwmMatches(ex_pwm, ar_er_seq)
#>  ESR1  ANDR FOXA1 ZN143 ZN281 
#>    62    61   334     1    63