get_literature_score: get_literature_score

In lubianat/iscore: Automatic calculation of literature relevance of genes

Description

Calculates the importance score for a given gene. The importance score is the total counts of articles in the pubmed database that are a result for that gene AND each term of a list

Usage

get_literature_score(
  genes,
  terms_of_interest,
  gene2pubmed = FALSE,
  return_all = FALSE,
  wait_time = 0,
  show_progress = TRUE,
  verbose = FALSE
)

Arguments

genes	A vector with multiple genes.
terms_of_interest	A list of terms of interest related to the topic you want to find the relevance for
gene2pubmed	logical defining if gene2pubmed db is going to be used. If used, the vector of genes has to be of HUMAN genes in the hgcn_symbol format.
return_all	Only to be used with gene2pubmed! logical defining if the all_counts table is going to be returned here. Usually it is generated by the test_score function.
wait_time	How long should be the interval between two requests to the ENTREZ database when it fails. Defaults to 0. In seconds.
show_progress	If TRUE, a progress bar is displayed. Defaults to TRUE.
verbose	If TRUE, will display the index of the search occuring. Defaults to FALSE.

Value

A dataframe with the literature scores.

Examples

genes <- c('CD8A', 'CD4')
terms_of_interest <-
  c(
    "CD4 T cell",
    "CD14+ Monocyte",
    "B cell",
    "CD8 T cell",
    "FCGR3A+ Monocyte",
    "NK cell",
    "Dendritic cell",
    "Megakaryocyte",
    'immunity'
  )
get_literature_score(genes, terms_of_interest)

lubianat/iscore documentation built on March 14, 2021, 11:50 a.m.