write_homer_motif: Write Motif PWM in HOMER format

In robertamezquita/marge: API for HOMER in R for Genomic Analysis using Tidy Conventions

Description

Create a minimal HOMER formatted motif file based on PWM and required motif info.

Usage

write_homer_motif(
  motif_pwm,
  motif_name,
  log_odds_detection,
  consensus = NULL,
  file,
  append = TRUE
)

Arguments

motif_pwm	tibble with alphabet columns
motif_name	name of the sequence
log_odds_detection	the threshold for detecting given motif
consensus	the accepted consensus motif sequence [optional: calculated from pwm if not provided]
file	path to new motif file; suffix should be '.motif'
append	whether to overwrite existing file [default: TRUE, e.g. add on to existing file]

Value

nothing; called for its side-effect of producing HOMER motif file

Examples

## Not run: 
knw_pwm <- read_known_results("inst/extdata/knownResults.txt", homer_dir = FALSE)

## Write multiple motifs
pwalk(list(motif_pwm = knw_pwm$motif_pwm,
           motif_name = knw_pwm$motif_name,
           log_odds_detection = knw_pwm$log_odds_detection),
      write_homer_motif, file = "test.motif", append = TRUE)

## End(Not run)

robertamezquita/marge documentation built on Sept. 30, 2020, 6:15 a.m.