annotate_gcr: Add positional annotation to MSstats group comparison result
In tobiasko/posprot: Positional Proteomics in R

Description Usage Arguments Details Value Examples

This function takes a peptide-level group comparison result as output by MSstats::groupComparison and adds positional annotation to each peptide feature.

1	annotate_gcr(name, MSstats.GC, label)

`MSstats.GC`	MSstats group comparison result as generated by groupComparison()
`label`	Label (character) of the comparision
`name`	file name (character) of a fasta file in working directory

This function maps all peptide features to a reference proteome using their stripped aa sequence and perfect string matching. In addition, it determines the N-terminal modification status of each feature.

Important prerequisites:

This functions expects the results of a MSstats peptide-level significance analysis as input, since positional proteomics is a completely peptide centric approach.

Peptide-level significance analysis can be enforced easily by copying the content of PeptideSequence to ProteinName prior to calling MSstats::dataProcess().

This function returns a table (data.frame) in long format. For none proteotypic peptides this function returns multiple rows, each listing the peptide in a different positional context. This ensures that all possible peptide origins can be considered in the downstream analysis.