metaseqR: An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms.
Version 1.16.0

Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.

AuthorPanagiotis Moulos <moulos@fleming.gr>
Bioconductor views DifferentialExpression GeneExpression Normalization Preprocessing QualityControl RNASeq ReportWriting Software WorkflowStep
Date of publicationNone
MaintainerPanagiotis Moulos <moulos@fleming.gr>
LicenseGPL (>= 3)
Version1.16.0
URL http://www.fleming.gr
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("metaseqR")

Getting started

Package overview

Popular man pages

combine.simes: Combine p-values with Simes' method
diagplot.boxplot: Boxplots wrapper for the metaseqR package
diagplot.ftd: Create False (or True) Positive (or Negative) curves
downsample.counts: Downsample read counts
get.biotypes: Biotype converter
make.permutation: Create counts matrix permutations
normalize.deseq: Normalization based on the DESeq package
See all...

All man pages Function index File listing

Man pages

as.class.vector: Create a class vector
build.export: Results export builder
calc.f1score: Calculate the F1-score
calc.otr: Calculate the ratio TP/(FP+FN)
cddat: Old functions from NOISeq
cdplot: Old functions from NOISeq
check.contrast.format: Contrast validator
check.file.args: File argument validator
check.graphics.file: Check graphics file
check.graphics.type: Check plotting device
check.libsize: Library size validator
check.main.args: Main argument validator
check.num.args: Numeric argument validator
check.packages: Required packages validator
check.parallel: Parallel run validator
check.text.args: Text argument validator
combine.bonferroni: Combine p-values with Bonferroni's method
combine.maxp: Combine p-values using the maximum p-value
combine.minp: Combine p-values using the minimum p-value
combine.simes: Combine p-values with Simes' method
combine.weight: Combine p-values using weights
construct.gene.model: Assemble a gene model based on exon counts
diagplot.avg.ftd: Create average False (or True) Discovery curves
diagplot.boxplot: Boxplots wrapper for the metaseqR package
diagplot.cor: Summarized correlation plots
diagplot.de.heatmap: Diagnostic heatmap of differentially expressed genes
diagplot.edaseq: Diagnostic plots based on the EDASeq package
diagplot.filtered: Diagnostic plot for filtered genes
diagplot.ftd: Create False (or True) Positive (or Negative) curves
diagplot.mds: Multi-Dimensinal Scale plots or RNA-Seq samples
diagplot.metaseqr: Diagnostic plots for the metaseqR package
diagplot.noiseq: Diagnostic plots based on the NOISeq package
diagplot.noiseq.saturation: Simpler implementation of saturation plots inspired from...
diagplot.pairs: Massive X-Y, M-D correlation plots
diagplot.roc: Create basic ROC curves
diagplot.venn: Venn diagrams when performing meta-analysis
diagplot.volcano: (Interactive) volcano plots of differentially expressed genes
disp: Message displayer
downsample.counts: Downsample read counts
estimate.aufc.weights: Estimate AUFC weights
estimate.sim.params: Estimate negative binomial parameters from real data
filter.exons: Filter gene expression based on exon counts
filter.genes: Filter gene expression based on gene counts
filter.high: Filtering helper
filter.low: Filtering helper
fisher.method: Perform Fisher's Method for combining p-values
fisher.method.perm: Derive a p-value for a summary statistic of p-values by...
fisher.sum: A function to calculate Fisher's sum for a set of p-values
get.annotation: Annotation downloader
get.arg: Argument getter
get.biotypes: Biotype converter
get.bs.organism: Return a proper formatted BSgenome organism name
get.dataset: Annotation downloader helper
get.defaults: Default parameters for several metaseqr functions
get.ensembl.annotation: Ensembl annotation downloader
get.exon.attributes: Annotation downloader helper
get.gc.content: Return a named vector of GC-content for each genomic region
get.gene.attributes: Annotation downloader helper
get.host: Annotation downloader helper
get.preset.opts: Return several analysis options given an analysis preset
get.strict.biofilter: Group together a more strict biotype filter
get.ucsc.annotation: UCSC/RefSeq annotation downloader
get.ucsc.credentials: Return host, username and password for UCSC Genome Browser...
get.ucsc.dbl: Download annotation from UCSC servers, according to organism...
get.ucsc.organism: Return a proper formatted organism alias
get.ucsc.query: Return queries for the UCSC Genome Browser database,...
get.ucsc.tabledef: Get SQLite UCSC table defintions, according to organism and...
get.ucsc.tbl.tpl: Create SQLite UCSC table template defintions
get.valid.chrs: Annotation downloader helper
get.weights: Get precalculated statistical test weights
graphics.close: Close plotting device
graphics.open: Open plotting device
hg19.exon.counts: Human RNA-Seq data with three conditions, three samples
libsize.list.hg19: Human RNA-Seq data with three conditions, three samples
libsize.list.mm9: Mouse RNA-Seq data with two conditions, four samples
load.bs.genome: Loads (or downloads) the required BSGenome package
log2disp: Display value transformation
make.avg.expression: Calculates fold changes
make.contrast.list: Create contrast lists from contrast vectors
make.export.list: Intitialize output list
make.fold.change: Calculates fold changes
make.grid: Optimize rectangular grid plots
make.highcharts.points: Interactive volcano plot helper
make.html.body: HTML report helper
make.html.cells: HTML report helper
make.html.header: HTML report helper
make.html.rows: HTML report helper
make.html.table: HTML report helper
make.matrix: Results output build helper
make.path.struct: Project path constructor helper
make.permutation: Create counts matrix permutations
make.project.path: Project path constructor
make.report.messages: Initializer of report messages
make.sample.list: Creates sample list from file
make.sim.data.sd: Create simulated counts using the Soneson-Delorenzi method
make.sim.data.tcc: Create simulated counts using TCC package
make.stat: Calculates several statistices on read counts
make.transformation: Calculates several transformation of counts
make.venn.areas: Helper for Venn diagrams
make.venn.colorscheme: Helper for Venn diagrams
make.venn.counts: Helper for Venn diagrams
make.venn.pairs: Helper for Venn diagrams
meta.perm: Permutation tests for meta-analysis
metaseqr: The main metaseqr pipeline
metaseqR-package: The metaseqR Package
meta.test: Meta-analysis using several RNA-Seq statistics
meta.worker: Permutation tests helper
mlfo: MLE dispersion estimate
mm9.gene.counts: mouse RNA-Seq data with two conditions, four samples
nat2log: General value transformation
normalize.deseq: Normalization based on the DESeq package
normalize.edaseq: Normalization based on the EDASeq package
normalize.edger: Normalization based on the edgeR package
normalize.nbpseq: Normalization based on the NBPSeq package
normalize.noiseq: Normalization based on the NOISeq package
read2count: SAM/BAM/BED file reader helper for the metaseqr pipeline
read.targets: Creates sample list and BAM/BED file list from file
reduce.exons: Merges exons to create a unique set of exons for each gene
reduce.gene.data: Reduce the gene annotation in case of not all chromosomes...
sample.list.hg19: Human RNA-Seq data with three conditions, three samples
sample.list.mm9: Mouse RNA-Seq data with two conditions, four samples
set.arg: Argument setter
stat.bayseq: Statistical testing with baySeq
stat.deseq: Statistical testing with DESeq
stat.edger: Statistical testing with edgeR
stat.limma: Statistical testing with limma
stat.nbpseq: Statistical testing with NBPSeq
stat.noiseq: Statistical testing with NOISeq
validate.alg.args: Validate normalization and statistical algorithm arguments
validate.list.args: Validate list parameters for several metaseqR functions
wapply: List apply helper
wp.adjust: Multiple testing correction helper

Functions

as.class.vector Man page Source code
biasPlotToJSON Source code
bioDetectionToJSON Source code
bioSaturationToJSON Source code
boxplotToJSON Source code
build.export Man page Source code
calc.f1score Man page Source code
calc.otr Man page Source code
cddat Man page Source code
cdplot Man page Source code
check.contrast.format Man page Source code
check.file.args Man page Source code
check.graphics.file Man page Source code
check.graphics.type Man page Source code
check.libsize Man page Source code
check.main.args Man page Source code
check.num.args Man page Source code
check.packages Man page Source code
check.parallel Man page Source code
check.text.args Man page Source code
combine.bonferroni Man page Source code
combine.maxp Man page Source code
combine.minp Man page Source code
combine.simes Man page Source code
combine.weight Man page Source code
construct.gene.model Man page Source code
countsBioToJSON Source code
deprecated.warning Source code
diagplot.avg.ftd Man page Source code
diagplot.boxplot Man page Source code
diagplot.cor Man page Source code
diagplot.de.heatmap Man page Source code
diagplot.edaseq Man page Source code
diagplot.filtered Man page Source code
diagplot.ftd Man page Source code
diagplot.mds Man page Source code
diagplot.metaseqr Man page Source code
diagplot.noiseq Man page Source code
diagplot.noiseq.saturation Man page Source code
diagplot.pairs Man page Source code
diagplot.roc Man page Source code
diagplot.venn Man page Source code
diagplot.volcano Man page Source code
disp Man page Source code
downsample.counts Man page Source code
elap2human Source code
estimate.aufc.weights Man page Source code
estimate.sim.params Man page Source code
filter.exons Man page Source code
filter.genes Man page Source code
filter.high Man page Source code
filter.low Man page Source code
filteredToJSON Source code
fisher.method Man page Source code
fisher.method.perm Man page Source code
fisher.sum Man page Source code
get.alt.host Source code
get.annotation Man page Source code
get.arg Man page Source code
get.biotypes Man page Source code
get.bs.organism Man page Source code
get.dataset Man page Source code
get.defaults Man page Source code
get.ensembl.annotation Man page Source code
get.exon.attributes Man page Source code
get.gc.content Man page Source code
get.gene.attributes Man page Source code
get.host Man page Source code
get.preset.opts Man page Source code
get.strict.biofilter Man page Source code
get.ucsc.annotation Man page Source code
get.ucsc.credentials Man page Source code
get.ucsc.dbl Man page Source code
get.ucsc.organism Man page Source code
get.ucsc.query Man page Source code
get.ucsc.tabledef Man page Source code
get.ucsc.tbl.tpl Man page Source code
get.valid.chrs Man page Source code
get.weights Man page Source code
getColorScheme Source code
getColors Source code
getGroupColorScheme Source code
graphics.close Man page Source code
graphics.open Man page Source code
hg19.exon.counts Man page
libsize.list.hg19 Man page
libsize.list.mm9 Man page
load.bs.genome Man page Source code
log2disp Man page Source code
make.avg.expression Man page Source code
make.contrast.list Man page Source code
make.export.list Man page Source code
make.fold.change Man page Source code
make.grid Man page Source code
make.highcharts.points Man page Source code
make.html.body Man page Source code
make.html.cells Man page Source code
make.html.header Man page Source code
make.html.rows Man page Source code
make.html.table Man page Source code
make.matrix Man page Source code
make.path.struct Man page Source code
make.permutation Man page Source code
make.project.path Man page Source code
make.report.messages Man page Source code
make.sample.list Man page Source code
make.sim.data.sd Man page Source code
make.sim.data.tcc Man page Source code
make.stat Man page Source code
make.transformation Man page Source code
make.venn.areas Man page Source code
make.venn.colorscheme Man page Source code
make.venn.counts Man page Source code
make.venn.pairs Man page Source code
mdsToJSON Source code
meta.perm Man page Source code
meta.test Man page Source code
meta.worker Man page Source code
metaseqR Man page
metaseqR-package Man page
metaseqR.version Source code
metaseqr Man page Source code
metaseqr.main Man page
mlfo Man page Source code
mm9.gene.counts Man page
nat2log Man page Source code
normalize.deseq Man page Source code
normalize.edaseq Man page Source code
normalize.edger Man page Source code
normalize.nbpseq Man page Source code
normalize.noiseq Man page Source code
read.targets Man page Source code
read2count Man page Source code
readNoiseToJSON Source code
reduce.exons Man page Source code
reduce.gene.data Man page Source code
sample.list.hg19 Man page
sample.list.mm9 Man page
set.arg Man page Source code
stat.bayseq Man page Source code
stat.deseq Man page Source code
stat.edger Man page Source code
stat.limma Man page Source code
stat.nbpseq Man page Source code
stat.noiseq Man page Source code
stopwrap Source code
unquote_js_fun Source code
validate.alg.args Man page Source code
validate.list.args Man page Source code
volcanoToJSON Source code
wapply Man page Source code
warnwrap Source code
wp.adjust Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/metaseqR-package.R
R/metaseqr-data.R
R/metaseqr.annotation.R
R/metaseqr.argcheck.R
R/metaseqr.count.R
R/metaseqr.export.R
R/metaseqr.filter.R
R/metaseqr.json.R
R/metaseqr.main.R
R/metaseqr.meta.R
R/metaseqr.norm.R
R/metaseqr.plot.R
R/metaseqr.query.R
R/metaseqr.sim.R
R/metaseqr.stat.R
R/metaseqr.util.R
R/zzz.R
build
build/vignette.rds
data
data/datalist
data/hg19.exon.data.rda
data/mm9.gene.data.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/metaseqr-pdf.R
inst/doc/metaseqr-pdf.Rnw
inst/doc/metaseqr-pdf.pdf
inst/loader.gif
inst/logo.png
inst/metaseqr_report.html
inst/styles.css
inst/unitTests
inst/unitTests/test_estimate_aufc_weights.R
inst/unitTests/test_metaseqr.R
man
man/as.class.vector.Rd
man/build.export.Rd
man/calc.f1score.Rd
man/calc.otr.Rd
man/cddat.Rd
man/cdplot.Rd
man/check.contrast.format.Rd
man/check.file.args.Rd
man/check.graphics.file.Rd
man/check.graphics.type.Rd
man/check.libsize.Rd
man/check.main.args.Rd
man/check.num.args.Rd
man/check.packages.Rd
man/check.parallel.Rd
man/check.text.args.Rd
man/combine.bonferroni.Rd
man/combine.maxp.Rd
man/combine.minp.Rd
man/combine.simes.Rd
man/combine.weight.Rd
man/construct.gene.model.Rd
man/diagplot.avg.ftd.Rd
man/diagplot.boxplot.Rd
man/diagplot.cor.Rd
man/diagplot.de.heatmap.Rd
man/diagplot.edaseq.Rd
man/diagplot.filtered.Rd
man/diagplot.ftd.Rd
man/diagplot.mds.Rd
man/diagplot.metaseqr.Rd
man/diagplot.noiseq.Rd
man/diagplot.noiseq.saturation.Rd
man/diagplot.pairs.Rd
man/diagplot.roc.Rd
man/diagplot.venn.Rd
man/diagplot.volcano.Rd
man/disp.Rd
man/downsample.counts.Rd
man/estimate.aufc.weights.Rd
man/estimate.sim.params.Rd
man/filter.exons.Rd
man/filter.genes.Rd
man/filter.high.Rd
man/filter.low.Rd
man/fisher.method.Rd
man/fisher.method.perm.Rd
man/fisher.sum.Rd
man/get.annotation.Rd
man/get.arg.Rd
man/get.biotypes.Rd
man/get.bs.organism.Rd
man/get.dataset.Rd
man/get.defaults.Rd
man/get.ensembl.annotation.Rd
man/get.exon.attributes.Rd
man/get.gc.content.Rd
man/get.gene.attributes.Rd
man/get.host.Rd
man/get.preset.opts.Rd
man/get.strict.biofilter.Rd
man/get.ucsc.annotation.Rd
man/get.ucsc.credentials.Rd
man/get.ucsc.dbl.Rd
man/get.ucsc.organism.Rd
man/get.ucsc.query.Rd
man/get.ucsc.tabledef.Rd
man/get.ucsc.tbl.tpl.Rd
man/get.valid.chrs.Rd
man/get.weights.Rd
man/graphics.close.Rd
man/graphics.open.Rd
man/hg19.exon.counts.Rd
man/libsize.list.hg19.Rd
man/libsize.list.mm9.Rd
man/load.bs.genome.Rd
man/log2disp.Rd
man/make.avg.expression.Rd
man/make.contrast.list.Rd
man/make.export.list.Rd
man/make.fold.change.Rd
man/make.grid.Rd
man/make.highcharts.points.Rd
man/make.html.body.Rd
man/make.html.cells.Rd
man/make.html.header.Rd
man/make.html.rows.Rd
man/make.html.table.Rd
man/make.matrix.Rd
man/make.path.struct.Rd
man/make.permutation.Rd
man/make.project.path.Rd
man/make.report.messages.Rd
man/make.sample.list.Rd
man/make.sim.data.sd.Rd
man/make.sim.data.tcc.Rd
man/make.stat.Rd
man/make.transformation.Rd
man/make.venn.areas.Rd
man/make.venn.colorscheme.Rd
man/make.venn.counts.Rd
man/make.venn.pairs.Rd
man/meta.perm.Rd
man/meta.test.Rd
man/meta.worker.Rd
man/metaseqR-package.Rd
man/metaseqr.Rd
man/mlfo.Rd
man/mm9.gene.counts.Rd
man/nat2log.Rd
man/normalize.deseq.Rd
man/normalize.edaseq.Rd
man/normalize.edger.Rd
man/normalize.nbpseq.Rd
man/normalize.noiseq.Rd
man/read.targets.Rd
man/read2count.Rd
man/reduce.exons.Rd
man/reduce.gene.data.Rd
man/sample.list.hg19.Rd
man/sample.list.mm9.Rd
man/set.arg.Rd
man/stat.bayseq.Rd
man/stat.deseq.Rd
man/stat.edger.Rd
man/stat.limma.Rd
man/stat.nbpseq.Rd
man/stat.noiseq.Rd
man/validate.alg.args.Rd
man/validate.list.args.Rd
man/wapply.Rd
man/wp.adjust.Rd
tests
tests/runTests.R
vignettes
vignettes/metaseqr-pdf.Rnw
metaseqR documentation built on May 20, 2017, 10:45 p.m.

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