Package: siggenes 1.87.0

Holger Schwender

siggenes: Multiple Testing using SAM and Efron's Empirical Bayes Approaches

Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).

Authors:Holger Schwender

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
siggenes/json (API)

# Install 'siggenes' in R:

install.packages('siggenes', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

On BioConductor:siggenes-1.87.0(bioc 3.24)siggenes-1.86.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

multiplecomparison microarray geneexpression snp exonarray differentialexpression

7.35 score 40 packages 94 scripts 72 mentions 51 exports 9 dependencies

Last updated from:817c2905c4. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	156
linux-devel-x86_64	NOTE	207
source / vignettes	OK	193
linux-release-x86_64	NOTE	198
macos-release-arm64	NOTE	92
macos-oldrel-arm64	NOTE	106
windows-devel	NOTE	114
windows-release	NOTE	111
windows-oldrel	NOTE	119
wasm-release	OK	103

Exports:args.ebam args.finda0 args.sam cat.ebam cat.stat chisq.ebam chisq.stat chisqClass d.stat denspr ebam ebam2excel ebam2html ebamControl find.a0 findDelta fudge2 fuzzy.ebam fuzzy.stat help.ebam help.finda0 help.sam identify limma2ebam limma2sam link.genes link.siggenes list.siggenes md.plot na.handling nclass.wand pi0.est plot plotArguments print qvalue.cal rowRanksWilc rowWilcoxon sam sam.plot2 sam2excel sam2html samControl show summary trend.ebam trend.stat wilc.ebam wilc.stat z.ebam z.find

Dependencies:Biobase BiocGenerics generics lattice MASS Matrix multtest scrime survival

siggenes Manual

Rendered fromsiggenes.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
EBAM Analysis for Categorical Data	cat.ebam chisq.ebam
SAM Analysis for Categorical Data	cat.stat chisq.stat
SAM Analysis Using a Modified t-statistic	d.stat
Delta Plots	delta.plot
Density Estimation	denspr
Empirical Bayes Analysis of Microarrays	ebam
Class EBAM	EBAM EBAM-class plot,EBAM,ANY-method plot,EBAM-method print,EBAM-method show,EBAM-method summary,EBAM-method
Further EBAM Arguments	ebamControl find.a0Control
Computation of the Fudge Factor	find.a0
Class FindA0	FindA0 FindA0-class plot,FindA0,ANY-method plot,FindA0-method print,FindA0-method show,FindA0-method
Finding the Threshold Delta	findDelta
Fudge Factor	fudge2
EBAM and SAM for Fuzzy Genotype Calls	fuzzy.ebam fuzzy.stat
Help files or argument list for EBAM-specific methods	args.ebam help.ebam
Help files or argument list for FindA0-specific methods	args.finda0 help.finda0
Help files or argument list for SAM-specific methods	args.sam help.sam
limma to SAM or EBAM	limma2ebam limma2sam
Links for a list of genes	link.genes
Links for a SAM or an EBAM object	link.siggenes
List of the significant genes	list.siggenes
MD Plot	md.plot
Number of cells in a histogram	nclass.wand
Estimation of the prior probability	pi0.est
Plot Arguments	plotArguments
Plot Arguments	plotFindArguments
Computation of the q-value	qvalue.cal
Rowwise Wilcoxon Rank Sum Statistics	rowRanksWilc rowWilcoxon
Significance Analysis of Microarray	sam
Class SAM	identify,SAM-method plot,SAM,ANY-method plot,SAM-method print,SAM-method SAM SAM-class show,SAM-method summary,SAM-method
SAM Plot	sam.plot2
Further SAM Arguments	samControl
CSV file of a SAM or an EBAM object	ebam2excel sam2excel siggenes2excel
HTML page for a SAM or an EBAM object	ebam2html sam2html siggenes2html
Classes sumSAM and sumEBAM	print,sumEBAM-method print,sumSAM-method show,sumEBAM-method show,sumSAM-method sumEBAM-class sumSAM-class
EBAM Analysis of Linear Trend	trend.ebam trend.ebam.data.frame trend.ebam.default trend.ebam.list
SAM Analysis of Linear Trend	trend.stat trend.stat.data.frame trend.stat.default trend.stat.list
EBAM Analysis Using Wilcoxon Rank Statistics	wilc.ebam
SAM Analysis Using Wilcoxon Rank Statistics	wilc.stat
EBAM analysis Using t- or F-test	z.ebam z.find