Map Motifs against a Motif Database.

Map Motifs against a Motif Database.

MotifCompare(
  motif.folder,
  known.motif,
  tomtom.path = NULL,
  tomtom.paras = "-no-ssc -min-overlap 5 -dist pearson -evalue -thresh 10.0",
  out.folder = NULL,
  show.html = TRUE
)

Arguments

motif.folder

Folder contains MotifDiscovery results.
known.motif

Motif database, should be in meme format.
tomtom.path

The path to MEME's tomtom. Default: NULL (conduct automatic detection).
tomtom.paras

Parameter for MEME's tomtom. Default: "-no-ssc -min-overlap 5 -dist pearson -evalue -thresh 10.0".
out.folder

Output folder. Default: NULL (current working directory).
show.html

Logical value, whether to show the results with pop-up window. Default: TRUE.

Value

Dataframe contains motif mapping results.

Examples

# library(DEbPeak)
# motif.cmp = MotifCompare(motif.folder = "/path/to/MotifDiscovery/out", known.motif = "/path/to/database.meme",
#                          tomtom.path = '/path/to/tomtom', out.folder = "/path/to/output")