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rnaSeqMap (version 2.30.0)

rnaSeq secondary analyses

Description

The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time

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Version

Version

2.30.0

License

GPL-2

Maintainer

Michal Okoniewski

Last Published

February 15th, 2017

Functions in rnaSeqMap (2.30.0)

RleList2matrix

RleList2matrix
regionCoverage

regionCoverage
generators

Generators for synt data and
findRegionsAsND

findRegionsAsND - finding regions of high coverage using Lindell-Aumann algorithm.
parseGff3

parseGff3 - parsing gff3 file format
rs.list

Example of sequencing data for rnaSeqMap library
spaceInChromosome

spaceInChromosome
getCoverageFromRS

getCoverageFromRS - conversion to coverage object
plotGeneCoverage

Genomic plots with rnaSeqMap
setData

Data accessor function for rnaSeqMap objects containing 'data' field
addExperimentsToReadset

addExperimentsToReadset - getting sample data from the database.
getBamData

getBamData - getting sample data from BAM file.
addDataToReadset

addDataToReadset - adding one more sample in the SeqRead on R level
simplePlot

simplePlot - quick plot for the coverages
NucleotideDistr-class

Numeric distributions by nucleotide - class
NDplots

Genomic plots based upon NucleotideDistr objects
measures

Measures
bam2sig

bam2sig - encapsulated pipeline of finding significant expression
normalizations

Normalization Methods
getExpDescription

getExpDescription
getFCFromND

getFCFromND - calculating fold change of coverages
regionBasedCoverage

regionBasedCoverage - transformation of the region coverage by the Lindell-Aumann regions
findRegionsAsIR

findRegionsAsIR - finding regions of high coverage using Lindell-Aumann algorithm.
normalizeBySum

Normalization of NucleotideDistr by global number of reads
buildDGEList

buildDGEList - create DGEList (edgeR)
setSAXPYData

Data accessor function for rnaSeqMap objects containing 'data' field
readsInRange

readsInRange
SeqReads

SeqReads - a container for RNAseq reads
buildDESeq

buildDESeq - create CountDataSet
averageND

averageND, sumND, combineNS, log2ND - operations on distributions
addBamData

addBamData - getting sample data from BAM file.
geneInChromosome

geneInChromosome
fiveCol2GRanges

fiveCol2GRanges
getSumsExp

getSumsExp
setSpecies

setSpecies
getData

Data accessor function for rnaSeqMap objects containing 'data' field
getSIFromND

getSIFromND - calculating splicing index of two coverages
gRanges2CamelMeasures

Genomic plots based upon NucleotideDistr objects