peptides which do not have protein assignment drop out
annotateAHO(pepseq, fasta)
| pepseq | - list of peptides - sequence, optional modified sequence, charge state. |
|---|---|
| fasta | - object as created by |
A data.frame with proteinID, peptideSeq, Offset and proteinSequence
library(dplyr) #> #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #> #> filter, lag #> The following objects are masked from 'package:base': #> #> intersect, setdiff, setequal, union 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")) resCanU <- resCan[!duplicated(unlist(resCan))] annotAll = annotateAHO(upeptide[seq_len(20)], resCanU) #> Joining, by = "proteinID" dim(annotAll) #> [1] 20 4