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metaseqR (version 1.12.2)

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

Description

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.

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Version

Version

1.12.2

License

GPL (>= 3)

Maintainer

Panagiotis Moulos

Last Published

February 15th, 2017

Functions in metaseqR (1.12.2)

diagplot.noiseq

Diagnostic plots based on the NOISeq package
combine.simes

Combine p-values with Simes' method
calc.otr

Calculate the ratio TP/(FP+FN)
cdplot

Old functions from NOISeq
diagplot.pairs

Massive X-Y, M-D correlation plots
diagplot.ftd

Create False (or True) Positive (or Negative) curves
combine.weight

Combine p-values using weights
diagplot.mds

Multi-Dimensinal Scale plots or RNA-Seq samples
combine.minp

Combine p-values using the minimum p-value
diagplot.roc

Create basic ROC curves
get.bs.organism

Return a proper formatted BSgenome organism name
estimate.aufc.weights

Estimate AUFC weights
diagplot.cor

Summarized correlation plots
get.exon.attributes

Annotation downloader helper
fisher.method.perm

Derive a p-value for a summary statistic of p-values by permutation
filter.high

Filtering helper
get.valid.chrs

Annotation downloader helper
get.ucsc.dbl

Download annotation from UCSC servers, according to organism and source
disp

Message displayer
stat.limma

Statistical testing with limma
get.ucsc.query

Return queries for the UCSC Genome Browser database, according to organism and source
graphics.close

Close plotting device
make.project.path

Project path constructor
metaseqR-package

The metaseqR Package
get.preset.opts

Return several analysis options given an analysis preset
make.permutation

Create counts matrix permutations
read.targets

Creates sample list and BAM/BED file list from file
normalize.nbpseq

Normalization based on the NBPSeq package
wapply

List apply helper
validate.alg.args

Validate normalization and statistical algorithm arguments
make.venn.colorscheme

Helper for Venn diagrams
get.gene.attributes

Annotation downloader helper
stat.nbpseq

Statistical testing with NBPSeq
check.parallel

Parallel run validator
construct.gene.model

Assemble a gene model based on exon counts
filter.genes

Filter gene expression based on gene counts
get.dataset

Annotation downloader helper
get.ucsc.credentials

Return host, username and password for UCSC Genome Browser database
make.matrix

Results output build helper
libsize.list.hg19

Human RNA-Seq data with three conditions, three samples
make.path.struct

Project path constructor helper
make.sim.data.sd

Create simulated counts using the Soneson-Delorenzi method
get.host

Annotation downloader helper
make.sim.data.tcc

Create simulated counts using TCC package
diagplot.boxplot

Boxplots wrapper for the metaseqR package
make.venn.counts

Helper for Venn diagrams
nat2log

General value transformation
filter.low

Filtering helper
make.venn.pairs

Helper for Venn diagrams
diagplot.venn

Venn diagrams when performing meta-analysis
reduce.exons

Merges exons to create a unique set of exons for each gene
get.ucsc.organism

Return a proper formatted organism alias
make.export.list

Intitialize output list
make.grid

Optimize rectangular grid plots
downsample.counts

Downsample read counts
make.report.messages

Initializer of report messages
get.weights

Get precalculated statistical test weights
mlfo

MLE dispersion estimate
combine.bonferroni

Combine p-values with Bonferroni's method
reduce.gene.data

Reduce the gene annotation in case of not all chromosomes present in counts
check.graphics.type

Check plotting device
sample.list.mm9

Mouse RNA-Seq data with two conditions, four samples
get.arg

Argument getter
diagplot.avg.ftd

Create average False (or True) Discovery curves
libsize.list.mm9

Mouse RNA-Seq data with two conditions, four samples
hg19.exon.counts

Human RNA-Seq data with three conditions, three samples
set.arg

Argument setter
check.packages

Required packages validator
validate.list.args

Validate list parameters for several metaseqR functions
diagplot.volcano

(Interactive) volcano plots of differentially expressed genes
diagplot.de.heatmap

Diagnostic heatmap of differentially expressed genes
mm9.gene.counts

mouse RNA-Seq data with two conditions, four samples
build.export

Results export builder
estimate.sim.params

Estimate negative binomial parameters from real data
stat.bayseq

Statistical testing with baySeq
get.defaults

Default parameters for several metaseqr functions
fisher.sum

A function to calculate Fisher's sum for a set of p-values
get.ucsc.annotation

UCSC/RefSeq annotation downloader
make.fold.change

Calculates fold changes
make.html.cells

HTML report helper
make.html.header

HTML report helper
make.contrast.list

Create contrast lists from contrast vectors
get.strict.biofilter

Group together a more strict biotype filter
meta.test

Meta-analysis using several RNA-Seq statistics
metaseqr

The main metaseqr pipeline
normalize.edaseq

Normalization based on the EDASeq package
normalize.deseq

Normalization based on the DESeq package
make.sample.list

Creates sample list from file
normalize.noiseq

Normalization based on the NOISeq package
stat.deseq

Statistical testing with DESeq
make.stat

Calculates several statistices on read counts
make.avg.expression

Calculates fold changes
check.libsize

Library size validator
check.contrast.format

Contrast validator
as.class.vector

Create a class vector
cddat

Old functions from NOISeq
check.text.args

Text argument validator
diagplot.edaseq

Diagnostic plots based on the EDASeq package
diagplot.filtered

Diagnostic plot for filtered genes
diagplot.noiseq.saturation

Simpler implementation of saturation plots inspired from NOISeq package
get.annotation

Annotation downloader
get.ensembl.annotation

Ensembl annotation downloader
log2disp

Display value transformation
get.ucsc.tabledef

Get SQLite UCSC table defintions, according to organism and source
fisher.method

Perform Fisher's Method for combining p-values
load.bs.genome

Loads (or downloads) the required BSGenome package
make.html.rows

HTML report helper
normalize.edger

Normalization based on the edgeR package
make.highcharts.points

Interactive volcano plot helper
get.ucsc.tbl.tpl

Create SQLite UCSC table template defintions
wp.adjust

Multiple testing correction helper
make.html.body

HTML report helper
check.num.args

Numeric argument validator
meta.worker

Permutation tests helper
stat.noiseq

Statistical testing with NOISeq
calc.f1score

Calculate the F1-score
check.graphics.file

Check graphics file
check.file.args

File argument validator
check.main.args

Main argument validator
combine.maxp

Combine p-values using the maximum p-value
diagplot.metaseqr

Diagnostic plots for the metaseqR package
filter.exons

Filter gene expression based on exon counts
get.biotypes

Biotype converter
get.gc.content

Return a named vector of GC-content for each genomic region
graphics.open

Open plotting device
make.html.table

HTML report helper
make.venn.areas

Helper for Venn diagrams
meta.perm

Permutation tests for meta-analysis
make.transformation

Calculates several transformation of counts
sample.list.hg19

Human RNA-Seq data with three conditions, three samples
read2count

SAM/BAM/BED file reader helper for the metaseqr pipeline
stat.edger

Statistical testing with edgeR