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

## Documentation for package ‘metaseqR’ version 1.20.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H L M N R S V W

metaseqR-package | The metaseqR Package

## -- A --

as.class.vector | Create a class vector

## -- B --

build.export | Results export builder

## -- C --

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
construct.utr.model | Assemble a gene model based on 3' UTR counts for quant-seq data

## -- D --

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 NOISeq package
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

## -- E --

estimate.aufc.weights | Estimate AUFC weights
estimate.sim.params | Estimate negative binomial parameters from real data

## -- F --

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 permutation
fisher.sum | A function to calculate Fisher's sum for a set of p-values

## -- G --

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.transcript.utr.attributes | Annotation downloader helper
get.ucsc.annotation | UCSC/RefSeq annotation downloader
get.ucsc.credentials | Return host, username and password for UCSC Genome Browser database
get.ucsc.dbl | Download annotation from UCSC servers, according to organism and source
get.ucsc.organism | Return a proper formatted organism alias
get.ucsc.query | Return queries for the UCSC Genome Browser database, according to organism and source
get.ucsc.tabledef | Get SQLite UCSC table defintions, according to organism and source
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

## -- H --

hg19.exon.counts | Human RNA-Seq data with three conditions, three samples

## -- L --

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

## -- M --

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
meta.test | Meta-analysis using several RNA-Seq statistics
meta.worker | Permutation tests helper
metaseqR | The metaseqR Package
metaseqr | The main metaseqr pipeline
metaseqr.main | The main metaseqr pipeline
mlfo | MLE dispersion estimate
mm9.gene.counts | mouse RNA-Seq data with two conditions, four samples

## -- N --

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

## -- R --

read.targets | Creates sample list and BAM/BED file list from file
read2count | SAM/BAM/BED file reader helper for the metaseqr pipeline
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 present in counts

## -- S --

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

## -- V --

validate.alg.args | Validate normalization and statistical algorithm arguments
validate.list.args | Validate list parameters for several metaseqR functions

## -- W --

wapply | List apply helper
wp.adjust | Multiple testing correction helper