find_motifs: Find motifs

In jiang-junyao/IReNA: IReNA

Find motifs

Description

Generate shell commands to find motifs in the footprints through fimo software.

Usage

find_motifs(
  motif,
  step = 20,
  fimodir,
  outputdir1,
  outputdir,
  Motifdir,
  sequencedir
)

Arguments

motif	motif file, you can choose our bulit-in motif database of 'mus musculus', 'homo sapiens', 'zebrafish' and 'chicken' by 'motif = Tranfac201803_Mm_MotifTFsF', 'motif = Tranfac201803_Hs_MotifTFsF', 'motif = Tranfac201803_Zf_MotifTFsF', 'motif = Tranfac201803_Ch_MotifTFsF' respectively, or you can upload your own motif data base, but the formata use be the same as our built-in motif database.
step	numeric, indicating the numbers of motif in each group. Because there are so many motifs need to be calculated, so we divided every 20 motifs into groups and then calculated each group using FIMO at the same time by nohup
fimodir	character, indicating path of fimo software, if you have added fimo to the environment variable, just set this argument as 'fimo'
outputdir1	character, indicating the output path of shell script
outputdir	character, indicating output path of fimo result
Motifdir	character, indicating the path of meme motif file
sequencedir	sequence file directory

Value

return scripts to run Fimo in command line

Examples

motif1 <- Tranfac201803_Mm_MotifTFsF
fimodir <- 'fimo'
outputdir <- 'D:/GIBH/IReNA2 R package/IReNA2/ATAC/outputdir/'
motifdir <- 'Mememotif/'
sequencedir <- 'merged_footprints.fasta'
#find_motifs(motif1,step=20,fimodir, outputdir, motifdir, sequencedir)

jiang-junyao/IReNA documentation built on Nov. 15, 2024, 1:51 a.m.