find_coDE: Find co-differentially expressed genes (co-DE genes)

In Ilarius/metaDEA: Perform co-DE gene analysis

Find co-differentially expressed genes (co-DE genes)

Description

Find all genes that are found differentially expressed in the same comparison(s).

Usage

find_coDE(gene, dataset)

Arguments

gene	a gene (character) included in one of the sublists in dataset. Can also be a vector of more than one gene, in that case only co-DE events including the genes in the vector will be reported.
dataset	list of lists, including a list called names containing sublists, each corresponding to a specific comparison from a study, of differentially expressed genes (each sublist is a character vector). The sublists should be named to identify the comparisons.

Value

a dataframe with 4 columns: gene1 and gene2 represent a co-DE gene pair; pair_occurrency indicates in how many comparisons a given co-DE gene pair is reported; comparisons lists these comparisons separated by ";". Results are sorted per pair_occurrency.

Examples

data(list_array) #load data
# create a list of lists were only the first 500 most significant genes with adjusted p-value < 0.05 and fold change >1.5 or < -1.5 are included
data(list_array) #load data
list_array.05_fc1.5_max500 <- subset_metanalysis(dataset=list_array, adjpval = 0.05, abslog2FC = log2(1.5), max_n_genes = 500 )
#find co-DE genes for the DYRK1A gene (ensemblID="ENSG00000157540")
head(find_coDE(gene="ENSG00000157540",dataset=list_array.05_fc1.5_max500))

Ilarius/metaDEA documentation built on May 6, 2023, 6:47 p.m.