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

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.

Author
Panagiotis Moulos <moulos@fleming.gr>
Date of publication
None
Maintainer
Panagiotis Moulos <moulos@fleming.gr>
License
GPL (>= 3)
Version
1.14.0
URLs

View on Bioconductor

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

Files in this package

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