# rnaSeq secondary analyses

## Documentation for package ‘rnaSeqMap’ version 2.32.0

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

## Help Pages

addBamData | addBamData - getting sample data from BAM file.
addDataToReadset | addDataToReadset - adding one more sample in the SeqRead on R level
addExperimentsToReadset | addExperimentsToReadset - getting sample data from the database.
allCamelMeasuresForRegion | Genomic plots based upon NucleotideDistr objects
averageND | averageND, sumND, combineNS, log2ND - operations on distributions
bam2sig | bam2sig - encapsulated pipeline of finding significant expression
buildDESeq | buildDESeq - create CountDataSet
buildDGEList | buildDGEList - create DGEList (edgeR)
combineND | averageND, sumND, combineNS, log2ND - operations on distributions
densityNormalize | Normalization Methods
diff_area | Measures
diff_derivative_area | Measures
distrCOVPlot | Genomic plots based upon NucleotideDistr objects
distrCOVPlotg | Genomic plots based upon NucleotideDistr objects
distribs | Numeric distributions by nucleotide - class
distrSIPlot | Genomic plots based upon NucleotideDistr objects
findRegionsAsIR | findRegionsAsIR - finding regions of high coverage using Lindell-Aumann algorithm.
findRegionsAsND | findRegionsAsND - finding regions of high coverage using Lindell-Aumann algorithm.
fiveCol2GRanges | fiveCol2GRanges
gcoverage | regionCoverage
geneInChromosome | geneInChromosome
generatorAdd | Generators for synt data and
generatorAddSquare | Generators for synt data and
generatorMultiply | Generators for synt data and
generatorPeak | Generators for synt data and
generatorSynth | Generators for synt data and
generatorTrunc | Generators for synt data and
getBamData | getBamData - getting sample data from BAM file.
getCoverageFromRS | getCoverageFromRS - conversion to coverage object
getData | Data accessor function for rnaSeqMap objects containing 'data' field
getDistr | Numeric distributions by nucleotide - class
getExpDescription | getExpDescription
getFCFromND | getFCFromND - calculating fold change of coverages
getSIFromND | getSIFromND - calculating splicing index of two coverages
getSumsExp | getSumsExp
ghistogram | Genomic plots with rnaSeqMap
globalCountsNormalize | Normalization Methods
gRanges2CamelMeasures | Genomic plots based upon NucleotideDistr objects
hump_diff1 | Measures
hump_diff2 | Measures
ks_test | Measures
log2ND | averageND, sumND, combineNS, log2ND - operations on distributions
min_maxNormalize | Normalization Methods
newNuctleotideDistr | Numeric distributions by nucleotide - class
newSeqReads | SeqReads - a container for RNAseq reads
newSeqReadsFromGene | SeqReads - a container for RNAseq reads
normalizeBySum | Normalization of NucleotideDistr by global number of reads
NucleotideDistr-class | Numeric distributions by nucleotide - class
parseGff3 | parseGff3 - parsing gff3 file format
plotCoverageHistogram | Genomic plots with rnaSeqMap
plotExonCoverage | Genomic plots with rnaSeqMap
plotGeneCoverage | Genomic plots with rnaSeqMap
plotGeneExonCoverage | Genomic plots with rnaSeqMap
plotRegionCoverage | Genomic plots with rnaSeqMap
plotSI | Genomic plots with rnaSeqMap
pp_derivative_plot | Measures
pp_plot | Measures
qq_derivative_plot | Measures
qq_plot | Measures
readsInRange | readsInRange
regionBasedCoverage | regionBasedCoverage - transformation of the region coverage by the Lindell-Aumann regions
regionCoverage | regionCoverage
regionmining | findRegionsAsND - finding regions of high coverage using Lindell-Aumann algorithm.
RleList2matrix | RleList2matrix
rs.list | Example of sequencing data for rnaSeqMap library
sample_data_rnaSeqMap | Example of sequencing data for rnaSeqMap library
SeqReads | SeqReads - a container for RNAseq reads
SeqReads-class | SeqReads - a container for RNAseq reads
setData | Data accessor function for rnaSeqMap objects containing 'data' field
setSAXPYData | Data accessor function for rnaSeqMap objects containing 'data' field
setSpecies | setSpecies
simplePlot | simplePlot - quick plot for the coverages
spaceInChromosome | spaceInChromosome
splicingind | getSIFromND - calculating splicing index of two coverages
standarizationNormalize | Normalization Methods
sumND | averageND, sumND, combineNS, log2ND - operations on distributions