test_score: Test the literature enrichment score

Description Usage Arguments Value Examples

Description

Test the literature enrichment score

Usage

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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

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# 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.