# Manipulating and exploring protein and proteomics data

## Documentation for package ‘Pbase’ version 0.22.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

aa | The 'Proteins' Class for Proteomics Data And Meta-Data
aa-method | The 'Proteins' Class for Proteomics Data And Meta-Data
acols | The 'Proteins' Class for Proteomics Data And Meta-Data
addIdentificationData-method | The 'Proteins' Class for Proteomics Data And Meta-Data
addPeptideFragments | The 'Proteins' Class for Proteomics Data And Meta-Data
addPeptideFragments-method | The 'Proteins' Class for Proteomics Data And Meta-Data
avarLabels | The 'Proteins' Class for Proteomics Data And Meta-Data
avarLabels-method | The 'Proteins' Class for Proteomics Data And Meta-Data
calculateHeavyLabels | Calculate heavy labeled peptides
class:Proteins | The 'Proteins' Class for Proteomics Data And Meta-Data
cleave-method | The 'Proteins' Class for Proteomics Data And Meta-Data
etrid2grl | From a transcript identifier to 'GRanges' object
isCleaved | The 'Proteins' Class for Proteomics Data And Meta-Data
isForward | Are all the ranges on the same strand
isReverse | Are all the ranges on the same strand
length-method | The 'Proteins' Class for Proteomics Data And Meta-Data
mapToGenome | Map range coordinates between proteins and genome space
mapToGenome-method | Map range coordinates between proteins and genome space
mapToGenome-methods | Map range coordinates between proteins and genome space
metadata-method | The 'Proteins' Class for Proteomics Data And Meta-Data
metadata<--method | The 'Proteins' Class for Proteomics Data And Meta-Data
names-method | The 'Proteins' Class for Proteomics Data And Meta-Data
p | Data accompanying the 'Pbase' package
pcols | The 'Proteins' Class for Proteomics Data And Meta-Data
pfeatures | The 'Proteins' Class for Proteomics Data And Meta-Data
pfeatures-method | The 'Proteins' Class for Proteomics Data And Meta-Data
pfilter | The 'Proteins' Class for Proteomics Data And Meta-Data
pfilter-method | The 'Proteins' Class for Proteomics Data And Meta-Data
plot-method | The 'Proteins' Class for Proteomics Data And Meta-Data
plotAsAnnotationTrack | Plot gene region and annotation tracks
plotAsGeneRegionTrack | Plot gene region and annotation tracks
pmapToGenome | Map range coordinates between proteins and genome space
pmapToGenome-method | Map range coordinates between proteins and genome space
pmapToGenome-methods | Map range coordinates between proteins and genome space
pms | Data accompanying the 'Pbase' package
Pparams | Class '"Pparams"'
Pparams-class | Class '"Pparams"'
pranges | The 'Proteins' Class for Proteomics Data And Meta-Data
pranges-method | The 'Proteins' Class for Proteomics Data And Meta-Data
pranges<- | The 'Proteins' Class for Proteomics Data And Meta-Data
pranges<--method | The 'Proteins' Class for Proteomics Data And Meta-Data
proteinCoding | Only keep protein coding ranges
proteinCoding-method | Only keep protein coding ranges
proteinCoding-methods | Only keep protein coding ranges
proteinCoverage | The 'Proteins' Class for Proteomics Data And Meta-Data
Proteins | The 'Proteins' Class for Proteomics Data And Meta-Data
Proteins-class | The 'Proteins' Class for Proteomics Data And Meta-Data
Proteins-method | The 'Proteins' Class for Proteomics Data And Meta-Data
proteotypic | The 'Proteins' Class for Proteomics Data And Meta-Data
pvarLabels | The 'Proteins' Class for Proteomics Data And Meta-Data
pvarLabels-method | The 'Proteins' Class for Proteomics Data And Meta-Data
rmEmptyRanges | The 'Proteins' Class for Proteomics Data And Meta-Data
seqnames-method | The 'Proteins' Class for Proteomics Data And Meta-Data
show-method | Class '"Pparams"'
show-method | The 'Proteins' Class for Proteomics Data And Meta-Data
[-method | The 'Proteins' Class for Proteomics Data And Meta-Data
[[-method | The 'Proteins' Class for Proteomics Data And Meta-Data