process_annotations: Process annotations

In AhmedMehdiLab/E.PAGE: Environmental Pathways Affecting Gene Expression

Process annotations

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, gs_filter = "")

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
gs_filter	optional: filter for gene set names

Value

gs_annos tibble: gene sets and annotations

annos vector: annotations

Examples

## Not run: 
anno_path <- system.file("extdata", "ex_anno.csv", package = "E.PAGE")
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)

AhmedMehdiLab/E.PAGE documentation built on Aug. 21, 2022, 4:37 p.m.