filter_original_regulation: filter original regulation

View source: R/scRNA1.R

filter_original_regulationR Documentation

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 Nov. 15, 2024, 1:51 a.m.