Find Motif of Peaks from RNA-seq and Peak-related Data Integrated Results.

Find Motif of Peaks from RNA-seq and Peak-related Data Integrated Results.

FindMotif(
  inte.res,
  peak.motif.key,
  peak.mode = c("consensus", "diff"),
  homer.motif.path = NULL,
  genome = "mm10",
  out.folder = NULL,
  other.paras = NULL
)

Arguments

inte.res	RNA and peak-related data integration results.
peak.motif.key	The key type of integrated results ("Type" column of inte.res) to find motif.
homer.motif.path	The path to Homer's findMotifsGenome.pl. Default: NULL (conduct automatic detection).
genome	Parameter for findMotifsGenome.pl, can be genome FASTA files or pre-build genome info. Default: mm10.
out.folder	The output folder. Default: NULL (current directory).
other.paras	Parameter for findMotifsGenome.pl, can be '-len 8,10,12 -size -100,50 -S 25'. Default: NULL.

Value

List contains known motif results of UPbATAC and DOWNbATAC.