get_literature_score {PubScore} | R Documentation |
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
get_literature_score(genes, terms_of_interest, gene2pubmed = FALSE, return_all = FALSE, wait_time = 0, show_progress = TRUE, verbose = FALSE)
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. |
A dataframe with the literature scores.
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)