Pbase: Manipulating and exploring protein and proteomics data
Version 0.16.0

A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.

AuthorLaurent Gatto [aut], Sebastian Gibb [aut, cre]
Bioconductor views DataImport DataRepresentation Infrastructure MassSpectrometry Proteomics Visualization
Date of publicationNone
MaintainerSebastian Gibb <mail@sebastiangibb.de>, Laurent Gatto <lg390@cam.ac.uk>
LicenseGPL-3
Version0.16.0
URL https://github.com/ComputationalProteomicsUnit/Pbase
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Pbase")

Getting started

`Pbase` example data

Popular man pages

coordinate-mapping-methods: Map range coordinates between proteins and genome space
isReverse: Are all the ranges on the same strand
p: Data accompanying the 'Pbase' package
plotAsAnnotationTrack: Plot gene region and annotation tracks
Pparams-class: Class '"Pparams"'
proteinCoding-methods: Only keep protein coding ranges
Proteins-class: The 'Proteins' Class for Proteomics Data And Meta-Data
See all...

All man pages Function index File listing

Man pages

calculateHeavyLabels: Calculate heavy labeled peptides
coordinate-mapping-methods: Map range coordinates between proteins and genome space
etrid2grl: From a transcript identifier to 'GRanges' object
isReverse: Are all the ranges on the same strand
p: Data accompanying the 'Pbase' package
plotAsAnnotationTrack: Plot gene region and annotation tracks
Pparams-class: Class '"Pparams"'
proteinCoding-methods: Only keep protein coding ranges
Proteins-class: The 'Proteins' Class for Proteomics Data And Meta-Data

Functions

Pparams Man page Source code
Pparams-class Man page
Proteins Man page
Proteins,EnsDb,missing-method Man page
Proteins,character,missing-method Man page
Proteins,missing,character-method Man page
Proteins,missing,missing-method Man page
Proteins-class Man page
[,Proteins,ANY,ANY,ANY-method Man page
[,Proteins,ANY,ANY-method Man page
[[,Proteins,ANY,ANY-method Man page
aa Man page Source code
aa,Proteins-method Man page
aaranges Source code
acols Man page Source code
addColumn Source code
addFastaInformation2mcol Source code
addIdentificationData,Proteins,character-method Man page
addIdentificationDataProteins Source code
addOverhangs Source code
addPeptideFragments Man page
addPeptideFragments,Proteins,character-method Man page
addPeptideFragmentsProteins Source code
avarLabels Man page Source code
avarLabels,Proteins-method Man page
biotypes Source code
calculateHeavyLabels Man page Source code
calculateIsoelectricPoint Source code
calculateMolecularWeight Source code
checkPcol Source code
class:Proteins Man page
cleave,Proteins-method Man page
createPbaseAccessionNumbers Source code
emptyProtDomIRanges Source code
etrid2grl Man page Source code
fastaCommentParser Source code
fastaComments2DataFrame Source code
featureToFilter Source code
flatIRangesList Source code
get.amino.acids Source code
get.atomic.mass Source code
get_pranges_indices Source code
htcat Source code
isCleaved Man page Source code
isForward Man page Source code
isReverse Man page Source code
length,Proteins-method Man page
mapToGenome Man page Source code
mapToGenome,ANY,ANY-method Man page
mapToGenome,Proteins,EnsDb-method Man page
mapToGenome,Proteins,GRangesList-method Man page
mapToGenome-methods Man page
mapToGenome2 Source code
mapplot Source code
metadata,Proteins-method Man page
metadata<-,Proteins-method Man page
names,Proteins-method Man page
onAttach Source code
p Man page
pcols Man page Source code
peptidePosition Source code
perlRxSubstring Source code
pfeatures Man page Source code
pfeatures,Proteins-method Man page
pfilter Man page
pfilter,Proteins-method Man page
pfilterProteins Source code
plot,Proteins,missing-method Man page
plotAsAnnotationTrack Man page Source code
plotAsGeneRegionTrack Man page Source code
plotProteins Source code
plotRanges Source code
pmapToGenome Man page
pmapToGenome,ANY,ANY-method Man page
pmapToGenome,Proteins,GRangesList-method Man page
pmapToGenome-methods Man page
pms Man page
pplot Source code
pranges Man page Source code
pranges,Proteins-method Man page
pranges<- Man page
pranges<-,Proteins,CompressedIRangesList-method Man page
proteinCoding Man page
proteinCoding,GRanges-method Man page
proteinCoding,GRangesList-method Man page
proteinCoding-methods Man page
proteinCoverage Man page Source code
proteotypic Man page Source code
pvarLabels Man page Source code
pvarLabels,Proteins-method Man page
readAAStringSet Source code
replaceAcols Source code
replacePranges Source code
rmEmptyRanges Man page Source code
sInRange Source code
sPbaseAccessionNumber Source code
sUniProtAccessionNumber Source code
sValidAccessionNumber Source code
sValidPeptide Source code
seqnames,Proteins-method Man page
setNames2 Source code
show,Pparams-method Man page
show,Proteins-method Man page
singleAA Source code
singular Source code
splitExonJunctions Source code
toBeImplemented Source code
tryCatchMapToGenome Source code
validProteins Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/AAStringSet-functions.R
R/AllClasses.R
R/AllGenerics.R
R/GRanges.R
R/Proteins-functions.R
R/Proteins-methods.R
R/coordinate-mapping-methods.R
R/environments.R
R/fasta-functions.R
R/heavylabels-functions.R
R/onAttach.R
R/params.R
R/peptides-functions.R
R/plotting.R
R/updateObject.R
R/utils.R
R/vigfigs.R
build
build/vignette.rds
data
data/datalist
data/p.rda
data/pms.rda
inst
inst/doc
inst/doc/Pbase-data.R
inst/doc/Pbase-data.Rmd
inst/doc/Pbase-data.html
inst/extdata
inst/extdata/01_test_database.fasta
inst/extdata/04_test_database.fasta
inst/extdata/HUMAN_2015_02_selected.fasta
inst/extdata/Thermo_Hela_PRTC_selected.mgf.gz
inst/extdata/Thermo_Hela_PRTC_selected.mzid
inst/extdata/heavylabels_groundtruth.csv
inst/extdata/heavylabels_proteins_of_interest.fasta
inst/scripts
inst/scripts/makep.R
inst/vignettes
inst/vignettes/Pbase-with-ensembldb.Rmd
inst/vignettes/ensucsc.Rmd
inst/vignettes/mapping.Rmd
man
man/Pparams-class.Rd
man/Proteins-class.Rd
man/calculateHeavyLabels.Rd
man/coordinate-mapping-methods.Rd
man/etrid2grl.Rd
man/isReverse.Rd
man/p.Rd
man/plotAsAnnotationTrack.Rd
man/proteinCoding-methods.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test_AAStringSet-functions.R
tests/testthat/test_Proteins-class.R
tests/testthat/test_Proteins-ensembldb.R
tests/testthat/test_Proteins-functions.R
tests/testthat/test_Proteins-methods.R
tests/testthat/test_fasta-functions.R
tests/testthat/test_heavylabels-functions.R
tests/testthat/test_mapToGenome-ensembldb.R
tests/testthat/test_peptides-functions.R
tests/testthat/test_utils.R
vignettes
vignettes/Pbase-data.Rmd
Pbase documentation built on May 20, 2017, 9:27 p.m.

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