Pbase API

[lgatto]

This is a list of (exported) symbols that are reviewed in the light of the new class implementation (see #38). Issue opened for progress tracking and general API discussion.

Constructor

• [x] Proteins(file = "missing", unitprotIds = "missing") ## empty object
• [x] Proteins(file = "character", unitprotIds = "missing") ## fasta file(s)
• [ ] Proteins(file = "missing", uniprotIds = "character") ## not yet implemented
• [ ] Proteins(file = "EnsDb", unitprotIds = "missing")

Accessors

• [x] seqnames, returns a character(n)
• [x] aa returns an AAStringSet (aa slot)
• [x] acols returns a DataFrame corresponding to the aa annotations
• [x] pcols returns a DataFrame corresponding to the pranges annotations
• [x] pranges returns a DataFrame with the IRangesList ranges
• [x] avarLabels returns the names of the sequence annotations (excluding the pranges names)
• [x] pvarLabels returns the names of the pranges
• [ ] an accessor for the pranges mcols.

Ranges:

• [x] aaranges (unexported)
• [x] pfeatures

Replacement functions

• [ ] acols(x) <-
• [ ] acols(x)$ <-
• [ ] pranges(x) <-
• [ ] pranges(x)$ <-

Processing

• [ ] cleave, isCleaved
• proteotypic
• proteinCoverage
• calculateHeavyLabels
• rmEmptyRanges
• pfilter
• addPeptideFragments

Mapping

• splitExonJunctions
• tryCatchMapToGenome
• proteinCoding
• pmapToGenome and pmapToGenome2
• maptoGenome
• isReverse and isForward
• etrid2grl
• biotype

Plotting

• [ ] plot
• [ ] plotAsGeneRegionTrack
• [ ] plotAsAnnotationTrack

Parameters

• Pparams

Deprecated

• pcols (pmetadata) should return a list of DataFrames, i.e. the mcols of the respective pranges. Something like lapply(pranges(x), mcols). Not sure if this is really useful at this stage.
• ametadata is the same as acols.

Internal and utils

• plotRanges
• htcat
• replaceAcols and replacePranges
• addacol and addpcol

[jorainer]

I would also add the Proteins(file = "EnsDb", unitprotIds = "missing") constructor to fetch the data from an EnsDb. Is mapToGenome now removed?

[lgatto]

Update. Feel free to modify the post above (or let me know if you can't).

[jorainer]

mapToGenome and pmapToGenome support now the pcol argument and work with the new Proteins objects.