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

Functions

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

Files

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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