filter_original_regulation: filter original regulation

In jiang-junyao/IReNA: IReNA

filter original regulation

Description

This function is used to further filter regulation generated by Genin3, PIDC, or other methods.

Usage

filter_original_regulation(
  potential_regulation,
  motif,
  tf_threshold = 500,
  target_threshold = 100
)

Arguments

potential_regulation	data.frame consists of three columns, first column contains source genes, second column contains target genes, third column contains weight.
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.
tf_threshold	the numbers of targets with highest weight of each transcription factor. Indicating the threshold to filter regulation.
target_threshold	numbers of top transcription factors for each target. Indicating the threshold to filter regulation.

jiang-junyao/IReNA documentation built on May 2, 2024, 6:54 a.m.