check_net_input {RITAN} | R Documentation |
A Quality Control function. This function will compare an input list of genes to a network reference and report if each member of the input is present in the resource.
check_net_input(set, ref, check4similar = FALSE, entity1name = "p1", entity2name = "p1")
set |
An input list of genes to check against a reference. |
ref |
A reference of network data. See readSIF(). |
check4similar |
Logical flag. If TRUE, a case-insensitive grep will be used for name matching. For genes in families with many related members (e.g. ABC*, FAM*, etc.), this will not be ideal. We intend this option as a QC screening method to identify if case, punctuaiton, etc is causing fewer than expected matches. |
entity1name |
The column name in "ref" of the first entity. Default = "p1." |
entity2name |
The column name in "ref" of the second entity. Default = "p2." |
Character vector of "yes/no" indicating "within-ref/not"
## Return a "yes/no" vector indicating if each gene in myGeneSet is annotated with any term in GO ## If no match, this function can attempt to suggest closest matches (check4similar = TRUE) library(RITANdata) myGeneSet <- c('BRCA1','RAD51C','VAV1','HRAS','ABCC1','CYP1B1','CYP3A5') yorn <- check_net_input( myGeneSet, network_list[["CCSB"]] ) print(yorn) yorn <- check_net_input( myGeneSet, network_list[["PID"]] ) print(yorn) ## See check_any_net_input() for efficiently checking across all resources.