plotResults-methods: Plot profiles of top genes/probes

In Rnits: R Normalization and Inference of Time Series data

Description

After fit has been applied on Rnits object, plot the profiles of N top ranking genes/probes.

Usage

plotResults(object, id = NULL, fdr = NULL, top = 48, pdf = FALSE,
  sort.by = "p-value", filename = "TopPlots.pdf", scale_y = NULL)

## S4 method for signature 'Rnits'
plotResults(object, id = NULL, fdr = NULL, top = 48,
  pdf = FALSE, sort.by = "p-value", filename = "TopPlots.pdf",
  scale_y = NULL)

Arguments

object	Rnits object.
id	Names of specific genes or probes to be plotted. Overrides fdr and top argument.
fdr	FDR cut-off plotting top probes or genes. Overrides top argument.
top	Number of top genes or probes whose profile is to be plotted. Default 48.
pdf	Save plot as pdf? Default FALSE.
sort.by	Criteria for sorting top genes or probes. Default 'p-value'.
filename	Name of pdf file. Default topplots.pdf.
scale_y	If 'free', use free scales for plots. Default NULL.
...	Optional arguments to plot

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)

# Plot top results
plotResults(rnitsobj, top = 16)


## End(Not run)

Rnits documentation built on Nov. 8, 2020, 6:26 p.m.