calculate_pre: Begin calculating overlap statistics

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

Description

Begin calculating overlap statistics

Usage

calculate_pre(input, annos, gs_annos, gs_genes)

Arguments

input	output of process_input_text or process_input_seurat
annos	value from process_annotations
gs_annos	value from process_annotations
gs_genes	value from process_database

Value

stats_pre tibble: overlap statistics (incomplete)

matches list: names: annotations vector: matched 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")
input <- process_input_text("FCN1 0.1 FTL 0.8 CLU 0.05")
calc_pre <- calculate_pre(input, anno_proc$annos, anno_proc$gs_annos,
                          data_proc$gs_genes)

## End(Not run)

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