rnaSeq secondary analyses


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Documentation for package ‘rnaSeqMap’ version 2.28.0

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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