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.

AuthorPanagiotis Moulos <moulos@fleming.gr>
Date of publicationNone
MaintainerPanagiotis Moulos <moulos@fleming.gr>
LicenseGPL (>= 3)
Version1.14.0
http://www.fleming.gr

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

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