Man pages for rnaSeqMap
rnaSeq secondary analyses
| addBamData | addBamData - getting sample data from BAM file. |
| addDataToReadset | addDataToReadset - adding one more sample in the SeqRead on R... |
| addExperimentsToReadset | addExperimentsToReadset - getting sample data from the... |
| averageND | averageND, sumND, combineNS, log2ND - operations on... |
| bam2sig | bam2sig - encapsulated pipeline of finding significant... |
| buildDESeq | buildDESeq - create CountDataSet |
| buildDGEList | buildDGEList - create DGEList (edgeR) |
| findRegionsAsIR | findRegionsAsIR - finding regions of high coverage using... |
| findRegionsAsND | findRegionsAsND - finding regions of high coverage using... |
| fiveCol2GRanges | fiveCol2GRanges |
| geneInChromosome | geneInChromosome |
| generators | 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... |
| getExpDescription | getExpDescription |
| getFCFromND | getFCFromND - calculating fold change of coverages |
| getSIFromND | getSIFromND - calculating splicing index of two coverages |
| getSumsExp | getSumsExp |
| gRanges2CamelMeasures | Genomic plots based upon NucleotideDistr objects |
| measures | Measures |
| NDplots | Genomic plots based upon NucleotideDistr objects |
| normalizations | Normalization Methods |
| normalizeBySum | Normalization of NucleotideDistr by global number of reads |
| NucleotideDistr-class | Numeric distributions by nucleotide - class |
| parseGff3 | parseGff3 - parsing gff3 file format |
| plotGeneCoverage | Genomic plots with rnaSeqMap |
| readsInRange | readsInRange |
| regionBasedCoverage | regionBasedCoverage - transformation of the region coverage... |
| regionCoverage | regionCoverage |
| RleList2matrix | RleList2matrix |
| rs.list | Example of sequencing data for rnaSeqMap library |
| SeqReds | SeqReads - a container for RNAseq reads |
| setData | Data accessor function for rnaSeqMap objects containing... |
| setSAXPYData | Data accessor function for rnaSeqMap objects containing... |
| setSpecies | setSpecies |
| simplePlot | simplePlot - quick plot for the coverages |
| spaceInChromosome | spaceInChromosome |
