VERBOSE: subset an expression dataset by extracting genes based on...

In montilab/BS831: Boston University - Genomics Data Mining

subset an expression dataset by extracting genes based on their level of variation

Description

subset an expression dataset by extracting genes based on their level of variation

Usage

VERBOSE(v, ...)

Arguments

dat	an expressionSet object
score	type of variation measure to use (can be 'mad', 'sd', or 'cv')
dir	direction of the gene ranking ('top': highest varying genes; 'bottom': lowest varying genes)
transform	transform the data before measuring variation
ngenes	number of top (or bottom) genes to extract
do.plot	plot the center vs. scale plot with selected genes highlighted
do.log	indicates whether to log the "x", "y", or "xy" axes, or "" none

Value

the filtered expressionSet object

Examples

# select the top 100 genes by median absolute deviation (mad) and also generate plot

# Use example data, for data set information: ?eSet.brca.100
data(eSet.brca.100)

variationFilter(eSet.brca.100,score='mad',ngenes=50,do.plot=TRUE)

montilab/BS831 documentation built on Feb. 4, 2025, 12:23 p.m.