compute: Perform computations on imported and processed data

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

Description

Perform computations on imported and processed data

Usage

compute(
  input,
  anno,
  data,
  universe = NULL,
  info_from = "database",
  anno_opts = "file",
  categories = FALSE,
  organisms = FALSE,
  save = NULL
)

Arguments

input	output of process_input_text or process_input_seurat
anno	output of import_annotations
data	output of import_database or import_msigdb
universe	number of genes in universe
info_from	optional: "annotation" or (default) "database"
anno_opts	optional: "name" for gene set names, "syms" for gene set symbols, "info" for gene set descriptions, "auto" for automatically generated annotations and/or (default) "file" for manual annotations
categories	optional: categories to include; default all
organisms	optional: organisms to include; default all
save	optional: path to save overlap statistics as .csv

Value

stats tibble: overlap statistics

matches list: names: annotations vector: matched genes

Examples

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)

input <- process_input_text('CYP1A1 0.2 CYP1B1 NQO1 0.3 SODD 9.0')
results <- compute(input, anno, data)

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