motifs_select: Select the motif related to the input genes

In jiang-junyao/IReNA: IReNA

Select the motif related to the input genes

Description

Select the motif related to the input genes. Genes used here should be ENSEMBEL ID.

Usage

motifs_select(motif, gene)

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.
gene	character, indicating genes used to filter motif. You can use differentially expressed genes of corresponding scRNA-seq or bulk RNA-seq data, or just use expressed genes.

Value

return filtered motif

Examples

load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
motif <- Tranfac201803_Hs_MotifTFsF
Kmeans_clustering_ENS <- add_ENSID(test_clustering, Spec1='Hs')
gene <- rownames(Kmeans_clustering_ENS)
filtered_motif <- motifs_select(motif,gene)

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