test_score {PubScore} | R Documentation |
Test the literature enrichment score
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 ") )
pub |
Object of class |
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). |
A "gg" object, from ggplot2, containing a network from the counts table.
# 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)