geneSetGPS: Highlight point (gene) position over a Multi-dimensional...

In chroGPS: chroGPS2: Generation, visualization and differential analysis of epigenome maps

Description

Given a list of genes of interest, the function highlights their position over a Multi-dimensional Scaling plot.

Usage

geneSetGPS(x, m, genes, uniqueCount = TRUE, ...)

Arguments

x	Matrix or data frame of observations x variables (tipically genes x epigenetic factors), with gene identifiers as rownames.
m	Object of class mds with a valid Multidimensional Scaling representation for the elements in x.
genes	Character vector containing gene identifiers, matching those on rownames(x).
uniqueCount	Set to FALSE if the MDS has been generated directly from the data in x, otherwise set to TRUE to match gene identifiers with their unique pattern of observed variables.
...	Additional parameters given to the generic function plot.

Value

Matrix with coordinates on the given input MDS object for the genes selected.

Author(s)

Oscar Reina

Examples

# Not run
# data(s2)
# d <- distGPS(s2.tab,metric='tanimoto',uniqueRows=TRUE)
# mds1 <- mds(d)
# set.seed(149)
# sampleGenes <- rownames(s2.tab)[sample(1:nrow(s2.tab),10,rep=FALSE)]
# pts <- geneSetGPS(s2.tab,mds1,genes=sampleGenes,uniqueCount=TRUE)
# plot(mds1)
# points(getPoints(pts),col='red',cex=3)

chroGPS documentation built on Oct. 31, 2019, 4:52 a.m.