View source: R/subset_metaanalysis.R
find_coDE | R Documentation |
Find all genes that are found differentially expressed in the same comparison(s).
find_coDE(gene, dataset)
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 |
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
.
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))
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