find_fold_changes_and_pvalues: Retrieve fold changes and adjusted-pvalues

In Ilarius/metaDEA: Perform co-DE gene analysis

Retrieve fold changes and adjusted-pvalues

Description

Retrieve for a given genes all the log2FCs and adjusted-p-values across the different comparison(s)

Usage

find_fold_changes_and_pvalues(gene, dataset)

Arguments

gene	a gene (character) included in one of the sublists in dataset.
dataset	list of 3 lists, the first with gene IDs (called names), the second with the adjusted p-values for each genes (called adjpval) and the third with log2 fold changes (called log2FC). Each one of these three lists have a number of sublists corresponding to the gene IDs, adjusted p-values, and log2FCs, respectively from the differential expression analyses of each comparison.

Value

a dataframe with 2 columns: log2FC and adjpval. Each row is a different comparison where the given gene is found DE.

Examples

# 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 )
#retrieve log2FCs and adjusted-p-values for the DYRK1A gene (ensemblID="ENSG00000157540")
find_fold_changes_and_pvalues(gene="ENSG00000157540",dataset=list_array.05_fc1.5_max500)

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