Description Usage Arguments Details Value Author(s) References
Get phosphorylation site localization probabilities by calling PhosphoRS
and parsing its output. getPhosphoRSProbabilities
generates a XML
input file for PhosphoRS calling writePhosphoRSInput
, then executes
phosphoRS.jar with java, and parses the XML result file with
readPhosphoRSOutput
.
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 | getPhosphoRSProbabilities(id.file, mgf.file, massTolerance, activationType,
simplify = FALSE, mapping.file = NULL, mapping =
c(peaklist = "even", id = "odd"), pepmodif.sep =
"##.##", besthit.only = TRUE, phosphors.cmd =
paste("java -jar", system.file("phosphors",
"phosphoRS.jar", package = "isobar")), file.basename =
tempfile("phosphors."))
writePhosphoRSInput(phosphoRS.infile, id.file, mgf.file, massTolerance,
activationType, mapping.file = NULL, mapping =
c(peaklist = "even", id = "odd"), pepmodif.sep =
"##.##", modif.masses = rbind(c("PHOS", "1",
"1:Phospho:Phospho:79.966331:PhosphoLoss:97.976896:STY"),
c("Oxidation_M", "2",
"2:Oxidation:Oxidation:15.994919:null:0:M"),
c("Cys_CAM", "3",
"3:Carbamidomethylation:Carbamidomethylation:57.021464:null:0:C"),
c("iTRAQ4plex", "4",
"4:iTRAQ4:iTRAQ4:144.1544:null:0:KX"), c("iTRAQ8plex",
"5", "5:iTRAQ8:iTRAQ8:304.308:null:0:KX"),
c("TMT6plex", "7",
"7:TMT6:TMT6:229.162932:null:0:KX"), c("TMTsixplex",
"6", "6:TMT6:TMT6:229.162932:null:0:KX")))
readPhosphoRSOutput(phosphoRS.outfile, simplify = FALSE, pepmodif.sep = "##.##", besthit.only = TRUE)
filterSpectraPhosphoRS(id.file, mgf.file, ..., min.prob = NULL, do.remove=FALSE)
|
id.file |
Database search results file in |
mgf.file |
Peaklist file |
massTolerance |
Fragment ion mass tolerance (in Da) |
activationType |
Activation types of spectra. CID, HCD, or ETD. |
simplify |
If |
mapping.file |
Mapping file. See also |
mapping |
Mapping columns. |
besthit.only |
Only show best hit, simplifies result to data.frame instead of list. |
phosphors.cmd |
PhosphoRS script. |
file.basename |
Base name for creating phosphoRS input and output files. |
phosphoRS.infile |
PhosphoRS input XML file name. |
phosphoRS.outfile |
PhosphoRS output XML file name. |
pepmodif.sep |
separator of peptide and modification in XML id |
modif.masses |
masses and ID used for PhosphoRS |
min.prob |
Threshold for PhosphoRS peptide probability to consider it for quantification |
... |
Further arguments to getPhosphoRSProbabilities |
do.remove |
If TRUE, spectra below the min.prob threshold are not just set as 'use.for.quant=FALSE' but removed. |
PhosphoRS is described in Taus et al., 2011. It can be downloaded from http://cores.imp.ac.at/protein-chemistry/download/ and used as Freeware. Java is required at runtime.
If simplify=TRUE
, a data.frame
with the following columns:
spectrum, peptide, modif, PepScore, PepProb, seqpos
If simplify=FALSE
, a list (of spectra) of lists (of peptide
identifications) of lists (with information about identification
and localization).
spectrum -> peptide 1, peptides 2, ... -> peptide.
First level:
- spectrum
Second level:
- peptide identifications for spectrum (might be more than one)
Third level:
- peptide: vector with peptide sequence and modification stirng
- site.probs: matrix with site probabilities for each phospho site
- isoforms: peptide score and probabilities for each isoform
Florian P Breitwieser
Taus et al., 2011
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