test_score: Test the literature enrichment score

In PubScore: Automatic calculation of literature relevance of genes

Description

Test the literature enrichment score

Usage

test_score(pub, total_genes, show_progress = TRUE,
  remove_ambiguous = TRUE, verbose = FALSE, nsim = 1e+05,
  ambiguous_terms = c("PC", "JUN", "IMPACT", "ACHE", "SRI", "SET", "CS",
  "PROC", "MET", "SHE", "CAD", "DDT", "PIGS", "SARS", "REST", "GC", "CP",
  "STAR", "SI", "GAN", "MARS", "SDS", "AGA", "NHS", "CPE", "POR", "MAX",
  "CAT", "LUM", "ANG", "POLE", "CLOCK", "TANK", "ITCH", "SDS", "AES",
  "CIC", "FST", "CAPS", "COPE", "F2", "AFM", "SPR", "PALM", "C2", "BAD",
  "GPI", "CA2", "SMS", "INVS", "WARS", "HP", "GAL", "SON", "AFM", "BORA",
  "MBP", "MAK", "MALL", "COIL", "CAST "))

## S4 method for signature 'PubScore'
test_score(pub, total_genes, show_progress = TRUE,
  remove_ambiguous = TRUE, verbose = FALSE, nsim = 1e+05,
  ambiguous_terms = c("PC", "JUN", "IMPACT", "ACHE", "SRI", "SET", "CS",
  "PROC", "MET", "SHE", "CAD", "DDT", "PIGS", "SARS", "REST", "GC", "CP",
  "STAR", "SI", "GAN", "MARS", "SDS", "AGA", "NHS", "CPE", "POR", "MAX",
  "CAT", "LUM", "ANG", "POLE", "CLOCK", "TANK", "ITCH", "SDS", "AES",
  "CIC", "FST", "CAPS", "COPE", "F2", "AFM", "SPR", "PALM", "C2", "BAD",
  "GPI", "CA2", "SMS", "INVS", "WARS", "HP", "GAL", "SON", "AFM", "BORA",
  "MBP", "MAK", "MALL", "COIL", "CAST "))

Arguments

pub	Object of class PubScore
total_genes	A list of all the possible genes in your study. Usually all the names in the rows of an "exprs" object.
show_progress	If TRUE, a progress bar is displayed. Defaults to True.
remove_ambiguous	If TRUE, ambiguously named genes (such as "MARCH") will be removed. Defaults to TRUE.
verbose	If TRUE, will display the index of the search occuring. Defaults to false.
nsim	The number of simulations to run. Defaults to 100000.
ambiguous_terms	A character vector of the ambiguous terms to use instead of the default. The default includes 60 genes pre-selected as ambiguous (as IMPACT, MARCH and ACHE).

Value

A "gg" object, from ggplot2, containing a network from the counts table.

Examples

# Create a new pubscore object
pub <- pubscore(genes = c('cd4','cd8'),
terms_of_interest = c('blabla','immunity'))
pub <- test_score(pub,
total_genes = c('notagene1', 'notagene2', 'cd4', 'cd8'),
remove_ambiguous = TRUE)

PubScore documentation built on Nov. 11, 2020, 2:01 a.m.