compute: Perform computations on imported and processed data

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

Perform computations on imported and processed data

Description

Perform computations on imported and processed data

Usage

compute(
  input,
  anno = E.PATH::annotations,
  data = E.PATH::database,
  universe = NULL,
  info_from = "database",
  anno_opts = "file",
  categories = FALSE,
  organisms = FALSE,
  org_db = NULL,
  save = NULL,
  gs_filter = ""
)

Arguments

input	output of process_input_text or process_input_seurat
anno	optional: E.PATH::annotations or output of import_annotations
data	optional: E.PATH::database or output of import_database
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
org_db	optional: GO organism database e.g. org.Hs.eg.db::org.Hs.eg.db
save	optional: path to save overlap statistics as .csv
gs_filter	optional: filter for gene set names

Value

stats tibble: overlap statistics

matches list: names: annotations vector: matched genes

Examples

input <- process_input_text("FCN1 0.1 FTL 0.8 CLU 0.05")
results <- compute(input)

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