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 |