process_annotations: Process annotations

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

Description

Choose annotations to include in annotation list, from gene set names, gene set symbols, gene set descriptions, annotations automatically extracted from gene set descriptions or manual annotations.

Usage

process_annotations(anno, info, options)

Arguments

anno	output of import_annotations
info	tibble: "name" gene set name "info" gene set descriptions
options	"name" for gene set names, "syms" for gene set symbols, "info" for gene set descriptions, "auto" for automatically generated annotations and/or "file" for manual annotations

Value

gs_annos tibble: gene sets and annotations

annos vector: annotations

Examples

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

anno_proc <- process_annotations(anno, info, "file")

## End(Not run)

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