Description Details Fields Methods Author(s) References See Also Examples
This class implements an R referenz class for BiblioSpec generated sqlite files and can return the data contained as data.frames or as list of tandem mass spectra peptide assignments objects (psm).
The function performs a SQL query on the SQLite files generated by BiblioSpec using the RSQLite package.
BiblioSpec files are generated by using Skyline or the BiblioSpec command line tool available from protwiz.
dbfile
database file location
getNrPSM()
Get number of psm's in database.
getPeaks(asList = FALSE)
Get peaks - mz and intensity and spectra id as data.frame.
getPsmSet()
get class psmSet S3 (list of psm objects). psm objects can be viewed by using the peakplot method of package protViz.
getSpectraMeta()
Get spectra meta information - retention time , file name, num peaks as data.frame
getSpectraWithMeta()
Get peaks with all the meta information as data.frame
summary()
summary of bibliospec file
Witold E. Wolski and Christian Panse
UNIT 13.7 Using BiblioSpec for Creating and Searching Tandem MS, Peptide Libraries. Barbara Frewen, Michael J. MacCoss. Current Protocols in Bioinformatics Current Protocols in Bioinformatics. http://dx.doi.org/10.1002/0471250953.bi1307s20.
The predecessor of the method getPsmSet
was implemented in
the bioconductor package specL:
Panse C, Trachsel C, Grossmann J and Schlapbach R. (2015). specL - An R/Bioconductor package to prepare peptide spectrum matches for use in targeted proteomics. Bioinformatics. http://dx.doi.org/10.1093/bioinformatics/btv105.
https://skyline.gs.washington.edu/labkey/project/home/software/Skyline/begin.view
https://skyline.gs.washington.edu/labkey/project/home/software/BiblioSpec/begin.view
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 | library(bibliospec)
# use the sqlite file provided in the package
dbfile <- file.path(path.package("bibliospec"),
"extdata/peptideStd.sqlite")
# call constructor
BS <- Bibliospec(dbfile=dbfile)
# test; should return TRUE
BS$getNrPSM() == 137
S <- BS$getPsmSet()
## Not run:
library(specL)
print(S)
lapply(S[1:10], plot)
## End(Not run)
peaks <- BS$getPeaks()
print(BS$summary())
head(peaks)
colnames(peaks)
spectrMet <- BS$getSpectraMeta()
dim(spectrMet)
alldata <- BS$getSpectraWithMeta()
alldata<- merge(spectrMet, peaks)
modification <- BS$getModification()
head(modification)
table(table(modification$RefSpectraID))
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