summary-methods: Summary of fit

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

Summary of fit

Description

Summarize top genes or probes from Rnits fit method

Usage

## S4 method for signature 'Rnits'
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)

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