Rnits (version 1.6.2)

summary,Rnits-method: Summary of fit

Description

Summarize top genes or probes from Rnits fit method

Usage

"summary"(object, top = 48, fdr = NULL, plot = FALSE, sort.by = "p-value")

Arguments

object

Rnits object on which fit has been applied

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

plot

If TRUE, plot histogram of p-values

sort.by

Sort top results by either p-value or FDR

Value

A table of top genes/profiles listing the ratio statistics, p-values, q-values and cluster information.

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 summary of top genes
# summary(rnitsobj, FDR = 5)
# 
# ## End(Not run)