The Proteins class encapsulates data and meta-data for proteomics experiments. The class stores the protein sequences as well as specific subsets of interest, typically peptides, as ranges. The Proteins instances, the sequence and peptide slots are described by their respective metadata attributes.
etrid2grl
(Package: Pbase) :
From a transcript identifier to code{GRanges
This function takes on or more Ensembl transcript identifiers, queries Biomart and constructs a GRangesList object as would Gviz::BiomartGeneRegionTrack for a genomic region (in fact, currently most of the code has been taken from Gviz::.fetchBMData and GViz::.chrName is used to validate chromosome names).
These functions convert ranges of peptides or exons to AnnotationTrack or GeneRegionTrack objects from the Gviz package and produces the corresponding plot. The genome argument controls whether additional ideogram and axis tracks are to be plotted. plotAsAnnotationTrack plots peptides that span multiple exons in red and connects them with a grey line. See pmapToGenome for example code.