get_cor: Calculate correlation of each gene pair, and remove genes...

In jiang-junyao/IReNA: IReNA

Calculate correlation of each gene pair, and remove genes that are below the threshold and are not transcription factors

Description

Calculate correlation of each gene pair, and remove genes that are below the threshold and are not transcription factors

Usage

get_cor(Kmeans_result, motif, correlation_filter, start_column = 4)

Arguments

Kmeans_result	Kmeans result, rownames should be ENSEMBL ID, first column should be Symbol ID, second column should be KmeansGroup
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.
correlation_filter	numeric, indicating correlation threshold
start_column	numeric, indicating the start column of expression value, defalut is 4

Value

return a table contain transcription factor with correlation > correlation_filter and correlation < -correlation_filter

Examples

load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
test_clustering=add_ENSID(test_clustering,Spec1 = 'Hs')
correlation <- get_cor(test_clustering, Tranfac201803_Hs_MotifTFsF, 0.7, start_column=3)

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