duplicateRemover: Remove duplicates in a named vector of phenotypes

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

Description

This function gets rid of the duplicates in a vector of phenotypes with gene identifiers as names. It is used to prepare the named vector of phenotypes for the over-representation and enrichment analysis.

Usage

duplicateRemover(geneList, method = "max")

Arguments

geneList

a single named numeric or integer vector with gene identifiers as names

method

a single character value specifying the method to remove the duplicates (should the minimum, maximum or average observation for a same construct be kept). The current version provides "min" (minimum), "max" (maximum), "average" and "fc.avg" (fold change average). The minimum and maximum should be understood in terms of absolute values (i.e. min/max effect, no matter the sign). The fold change average method converts the fold changes to ratios, averages them and converts the average back to a fold change.

Value

a named vector of phenotypes with duplicates removed

Author(s)

Camille Terfve, John C. Rose and Xin Wang

See Also

preprocess

Examples

x<-c(5,1,3,-2,6)
names(x)<-c("gene1","gene3","gene7","gene3","gene4")
xprocessed<-duplicateRemover(geneList=x,method="max")

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.