find_motifs_targetgenes: Use fimo to scan the TSS regions of candidate genes to find...
In jiang-junyao/IReNA: IReNA

find_motifs_targetgenes

R Documentation

Use fimo to scan the TSS regions of candidate genes to find binding motifs

Description

Use fimo to scan the TSS regions of candidate genes to find binding motifs

Usage

find_motifs_targetgenes(
  gene_tss,
  motif,
  refdir,
  fimodir,
  outputdir1,
  Motifdir,
  sequencedir = NULL,
  select_motif = T,
  use_nohup = F
)

Arguments

`gene_tss`	TSS region of genes. first column should be gene, second column should be chr, third column should be start, fourth column should be end. generated by `get_tss_region`
`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.
`refdir`	character, indicating the path of reference genome. Reference genome can be download from https://hgdownload.soe.ucsc.edu/downloads.html
`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 the shell scripts and sequence of target genes tss regions.(function 'find_motifs_targetgenes' will automatically generate two folders ('fasta' and 'fimo') in the path 'outputdir1', and store sequence of target genes tss regions in the 'fasta' and shell scripts in the 'fimo')
`Motifdir`	character, indicating the path of meme motif file
`sequencedir`	character, indicating the path of sequence of target genes tss regions. If it's NULL, this parameter will be paste0(outputdir1,'fasta/')
`select_motif`	logic, indicating whether to select motifs whose related transcription factors are in genes of gene_tss
`use_nohup`	logic, indicating whether use nohup to run all fimo scripts simultaneously