meshTable: Build a two-column word/frequency table

In shbrief/PCAGenomicSignatures: Interpretation of RNA-seq experiments through robust, efficient comparison to public databases

Build a two-column word/frequency table

Description

Build a two-column word/frequency table

Usage

meshTable(
  RAVmodel,
  ind,
  rm.noise = NULL,
  weighted = TRUE,
  filterMessage = 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.
filterMessage	A logical. Under the default TRUE, any output RAV belong to the filtering list will give a message. Silence this message with filterMessage=FALSE. You can check the filter list using data("filterList").

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)

shbrief/PCAGenomicSignatures documentation built on May 3, 2023, 11:21 a.m.