duplicateRemover: Remove duplicates in a named vector of phenotypes.

In CityUHK-CompBio/HTSanalyzeR2: HTSanalyzeR2: An R package for functional annotation, network analysis and time series analysis of high-throughput data

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 gene set 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.

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")

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 3, 2020, 2:35 a.m.