peptides which do not have protein assignment drop out
annotatePeptides( pepinfo, fasta, peptide = "peptideSeq", prefix = "(([RK])|(^)|(^M))", suffix = "" )
| pepinfo | - list of peptides - sequence, optional modified sequence, charge state. |
|---|---|
| fasta | - object as created by readPeptideFasta |
| peptide | - name of column containing peptide sequences default "peptideSeq" |
| prefix | - default "(([RK])|(^)|(^M))" |
| suffix | - default "" |
data.frame with columns "peptideSeq", "proteinID","Offset","proteinSequence","matched", "lengthPeptide","proteinlength"
library(dplyr) file = system.file("extdata/IDResults.txt.gz" , package = "prozor") specMeta <- readr::read_tsv(file) #> Rows: 5000 Columns: 12 #> -- Column specification -------------------------------------------------------- #> Delimiter: "\t" #> chr (2): peptideSeq, peptideModSeq #> dbl (10): RefSpectraId, numPeaks, precursorCharge, precursorMZ, retentionTim... #> #> i Use `spec()` to retrieve the full column specification for this data. #> i Specify the column types or set `show_col_types = FALSE` to quiet this message. upeptide <- unique(specMeta$peptideSeq) resCan <- prozor::readPeptideFasta( system.file("p1000_db1_example/Annotation_canSeq.fasta.gz" , package = "prozor")) annotAll = prozor::annotatePeptides(upeptide[seq_len(20)], resCan) #> Warning: `funs()` was deprecated in dplyr 0.8.0. #> Please use a list of either functions or lambdas: #> #> # Simple named list: #> list(mean = mean, median = median) #> #> # Auto named with `tibble::lst()`: #> tibble::lst(mean, median) #> #> # Using lambdas #> list(~ mean(., trim = .2), ~ median(., na.rm = TRUE)) #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was generated. #> Joining, by = "proteinID" dim(annotAll) #> [1] 20 6 res <- mutate(annotAll, proteinlength = nchar(proteinSequence)) res <- select(res, proteinID, peptideSeq, proteinlength, Offset, lengthPeptide) head(res) #> proteinID peptideSeq proteinlength Offset #> 1 sp|P02765|FETUA_HUMAN AQLVPLPPSTYVEFTVSGTDCVAK 367 188 #> 2 sp|P06396|GELS_HUMAN AQPVQVAEGSEPDGFWEALGGK 782 627 #> 3 sp|P01011|AACT_HUMAN AVLDVFEEGTEASAATAVK 423 361 #> 4 sp|P02787|TRFE_HUMAN CSTSSLLEACTFR 698 684 #> 5 sp|P01011|AACT_HUMAN EIGELYLPK 423 307 #> 6 sp|P01767|HV353_HUMAN EVQLVETGGGLIQPGGSLR 116 20 #> lengthPeptide #> 1 24 #> 2 22 #> 3 19 #> 4 13 #> 5 9 #> 6 19