explore_annotation: Find an annotation's associated gene sets and genes

In lilin-yang/glacier: Gene List Annotation, Calculation and Illustration of Enrichment in R

Description

Find an annotation's associated gene sets and genes

Usage

explore_annotation(annotation, gs_annos, gs_genes, genes = NULL)

Arguments

annotation	annotation to explore
gs_annos	value from process_annotations
gs_genes	value from process_database
genes	optional: genes to match, or (default) all

Value

"names" vector: gene set names

"genes" vector: genes

Examples

## Not run: 
anno_path <- system.file("extdata", "ex_anno.csv", package = "glacier")
data_path <- system.file("extdata", "ex_data.csv", package = "glacier")
anno <- import_annotations(anno_path, ",", TRUE, c(2, 4), 5)
data <- import_database(data_path, ",", FALSE, c(2, 4), 0)
info <- anno[c("name", "info")]

anno_proc <- process_annotations(anno, info, "file")
data_proc <- process_database(data, "Not assigned", "Not assigned")
anno_assoc <- explore_annotation("Carcinogen", anno_proc$gs_annos,
                                 data_proc$gs_genes)

## End(Not run)

lilin-yang/glacier documentation built on Oct. 3, 2020, 8:06 a.m.