meshTable {GenomicSuperSignature}R Documentation

Build a two-column word/frequency table

Description

Build a two-column word/frequency table

Usage

meshTable(RAVmodel, ind, rm.noise = NULL, weighted = TRUE)

Arguments

RAVmodel

A PCAGenomicSignatures object

ind

An index of RAV

rm.noise

An integer. Under the default (rm.noise=NULL), if cluster size (= s) is smaller than 8, rm.noise = floor(s*0.5). For clusters with >= 8 PCs, rm.noise = 4. If rm.noise = 0, all the MeSH terms in RAV will be used to draw wordcloud.

weighted

A logical. If TRUE, MeSH terms from each study are weighted based on the variance explained by the principle component of the study contributing a give RAV. Default is TRUE.

Value

A table with two columns, word and freq. MeSH terms in the defined RAV (by ind argument) is ordered based on their frequency.

Examples

data(miniRAVmodel)
meshTable(miniRAVmodel,1139)


[Package GenomicSuperSignature version 1.2.1 Index]