R/FurtherAnalysis.R

In protViz/bibliospec: Reading and Analyzing Mass Spectrometric Search Results

#-- count nr of peptide protein assigments

.ProteotypicCountView <- "create view ProteotypicCount as
select * from
(Select peptideSeq, count(*) as Freq from PeptideAnnotation group by peptideSeq) as peptide
inner join
RefSpectra
on RefSpectra.peptideSeq = peptide.peptideSeq"



#-- assign spectra matching proteotypic peptides to proteins.
.ProteinsView <- "create view Proteins as 
select * from
(select * from ProteotypicCount where Freq == 1) as Proteotypic
INNER join
PeptideAnnotation
on Proteotypic.peptideSeq = PeptideAnnotation.peptideSeq"