topData-methods: Data of top genes/probes

In dipenps/rnits: R Normalization and Inference of Time Series data

Data of top genes/probes

Description

Extract expression data for top genes/probes

Usage

topData(object, id = NULL, fdr = NULL, top = 16, sort.by = "p-value")

## S4 method for signature 'Rnits'
topData(object, id = NULL, fdr = NULL, top = 16,
  sort.by = "p-value")

Arguments

object	Rnits object on which fit has been applied
id	Names of probes or genes
top	Display results for top N genes/probes. Default 50
fdr	Display results for genes/probes less than FDR cutoff (if provided). Overrides top argument
sort.by	Sort top results by either p-value or FDR

Value

A table of expression values of top genes/profiles

Examples

# load pre-compiled expressionSet object for Ronen and Botstein yeast  chemostat data
data(yeastchemostat)
rnitsobj = build.Rnits(yeastchemostat, logscale = TRUE, normmethod = 'Between')
## Not run: 
# Fit model using gene-level summarization
rnitsobj <- fit(rnitsobj, gene.level = TRUE, clusterallsamples = FALSE)

#Get data for top genes
td <- topData(rnitsobj, FDR = 5)


## End(Not run)

dipenps/rnits documentation built on March 18, 2023, 7:30 p.m.