check_net_input: check_net_input

In MTZimmer/RITAN: Rapid Integration of Term Annotation and Network resources

Description

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.

Usage

check_net_input(set, ref, check4similar = FALSE, entity1name = "p1",
  entity2name = "p1")

Arguments

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."

Value

Character vector of "yes/no" indicating "within-ref/not"

Examples

## 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.

MTZimmer/RITAN documentation built on Feb. 21, 2020, 7:09 a.m.