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

as.class.vectorCreate a class vector
build.exportResults export builder
calc.f1scoreCalculate the F1-score
calc.otrCalculate the ratio TP/(FP+FN)
cddatOld functions from NOISeq
cdplotOld functions from NOISeq
check.contrast.formatContrast validator
check.file.argsFile argument validator graphics file plotting device
check.libsizeLibrary size validator
check.main.argsMain argument validator
check.num.argsNumeric argument validator
check.packagesRequired packages validator
check.parallelParallel run validator
check.text.argsText argument validator
combine.bonferroniCombine p-values with Bonferroni's method
combine.maxpCombine p-values using the maximum p-value
combine.minpCombine p-values using the minimum p-value
combine.simesCombine p-values with Simes' method
combine.weightCombine p-values using weights
construct.gene.modelAssemble a gene model based on exon counts
construct.utr.modelAssemble a gene model based on 3' UTR counts for quant-seq...
diagplot.avg.ftdCreate average False (or True) Discovery curves
diagplot.boxplotBoxplots wrapper for the metaseqR package
diagplot.corSummarized correlation plots heatmap of differentially expressed genes
diagplot.edaseqDiagnostic plots based on the EDASeq package
diagplot.filteredDiagnostic plot for filtered genes
diagplot.ftdCreate False (or True) Positive (or Negative) curves
diagplot.mdsMulti-Dimensinal Scale plots or RNA-Seq samples
diagplot.metaseqrDiagnostic plots for the metaseqR package
diagplot.noiseqDiagnostic plots based on the NOISeq package
diagplot.noiseq.saturationSimpler implementation of saturation plots inspired from...
diagplot.pairsMassive X-Y, M-D correlation plots
diagplot.rocCreate basic ROC curves
diagplot.vennVenn diagrams when performing meta-analysis
diagplot.volcano(Interactive) volcano plots of differentially expressed genes
dispMessage displayer
downsample.countsDownsample read counts
estimate.aufc.weightsEstimate AUFC weights
estimate.sim.paramsEstimate negative binomial parameters from real data
filter.exonsFilter gene expression based on exon counts
filter.genesFilter gene expression based on gene counts
filter.highFiltering helper
filter.lowFiltering helper
fisher.methodPerform Fisher's Method for combining p-values
fisher.method.permDerive a p-value for a summary statistic of p-values by...
fisher.sumA function to calculate Fisher's sum for a set of p-values
get.annotationAnnotation downloader
get.argArgument getter
get.biotypesBiotype converter a proper formatted BSgenome organism name
get.datasetAnnotation downloader helper
get.defaultsDefault parameters for several metaseqr functions
get.ensembl.annotationEnsembl annotation downloader
get.exon.attributesAnnotation downloader helper
get.gc.contentReturn a named vector of GC-content for each genomic region
get.gene.attributesAnnotation downloader helper
get.hostAnnotation downloader helper
get.preset.optsReturn several analysis options given an analysis preset
get.strict.biofilterGroup together a more strict biotype filter
get.transcript.utr.attributesAnnotation downloader helper
get.ucsc.annotationUCSC/RefSeq annotation downloader
get.ucsc.credentialsReturn host, username and password for UCSC Genome Browser...
get.ucsc.dblDownload annotation from UCSC servers, according to organism...
get.ucsc.organismReturn a proper formatted organism alias
get.ucsc.queryReturn queries for the UCSC Genome Browser database,...
get.ucsc.tabledefGet SQLite UCSC table defintions, according to organism and...
get.ucsc.tbl.tplCreate SQLite UCSC table template defintions
get.valid.chrsAnnotation downloader helper
get.weightsGet precalculated statistical test weights
graphics.closeClose plotting device
graphics.openOpen plotting device
hg19.exon.countsHuman RNA-Seq data with three conditions, three samples
libsize.list.hg19Human RNA-Seq data with three conditions, three samples
libsize.list.mm9Mouse RNA-Seq data with two conditions, four samples (or downloads) the required BSGenome package
log2dispDisplay value transformation
make.avg.expressionCalculates fold changes
make.contrast.listCreate contrast lists from contrast vectors
make.export.listIntitialize output list
make.fold.changeCalculates fold changes
make.gridOptimize rectangular grid plots
make.highcharts.pointsInteractive volcano plot helper
make.html.bodyHTML report helper
make.html.cellsHTML report helper
make.html.headerHTML report helper
make.html.rowsHTML report helper
make.html.tableHTML report helper
make.matrixResults output build helper
make.path.structProject path constructor helper
make.permutationCreate counts matrix permutations
make.project.pathProject path constructor of report messages
make.sample.listCreates sample list from file simulated counts using the Soneson-Delorenzi method simulated counts using TCC package
make.statCalculates several statistices on read counts
make.transformationCalculates several transformation of counts
make.venn.areasHelper for Venn diagrams
make.venn.colorschemeHelper for Venn diagrams
make.venn.countsHelper for Venn diagrams
make.venn.pairsHelper for Venn diagrams
meta.permPermutation tests for meta-analysis
metaseqrThe main metaseqr pipeline
metaseqR-packageThe metaseqR Package
meta.testMeta-analysis using several RNA-Seq statistics
meta.workerPermutation tests helper
mlfoMLE dispersion estimate
mm9.gene.countsmouse RNA-Seq data with two conditions, four samples
nat2logGeneral value transformation
normalize.deseqNormalization based on the DESeq package
normalize.edaseqNormalization based on the EDASeq package
normalize.edgerNormalization based on the edgeR package
normalize.nbpseqNormalization based on the NBPSeq package
normalize.noiseqNormalization based on the NOISeq package
read2countSAM/BAM/BED file reader helper for the metaseqr pipeline
read.targetsCreates sample list and BAM/BED file list from file
reduce.exonsMerges exons to create a unique set of exons for each gene
reduce.gene.dataReduce the gene annotation in case of not all chromosomes...
sample.list.hg19Human RNA-Seq data with three conditions, three samples
sample.list.mm9Mouse RNA-Seq data with two conditions, four samples
set.argArgument setter
stat.bayseqStatistical testing with baySeq
stat.deseqStatistical testing with DESeq
stat.edgerStatistical testing with edgeR
stat.limmaStatistical testing with limma
stat.nbpseqStatistical testing with NBPSeq
stat.noiseqStatistical testing with NOISeq
validate.alg.argsValidate normalization and statistical algorithm arguments
validate.list.argsValidate list parameters for several metaseqR functions
wapplyList apply helper
wp.adjustMultiple testing correction helper
pmoulos/metaseqR documentation built on Oct. 23, 2017, 1:18 p.m.