isobar-import: Loading data into IBSpectra objects using readIBSpectra
In isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description Usage Arguments Author(s) See Also Examples

Read ibspectra-csv files and peaklist files as an IBSpectra object of type 'type' (see IBSpectra, e.g. iTRAQ4plexSpectra or TMT6plexSpectra). If peaklist.file is missing, it is assumed that id.file contains intensity and m/z columns for the reporter tags.

## S4 method for signature 'character,character'
readIBSpectra(type,id.file)

# reads id file
## S4 method for signature 'character,character,character'
readIBSpectra(
                 type, id.file, peaklist.file, sep = "\t", mapping.file
                 = NULL, mapping = c(quantification.spectrum = "hcd",
                 identification.spectrum = "cid"), id.file.domap =
                 NULL, identifications.format = NULL, decode.titles =
                 FALSE, ...)

# reads peaklist file
## S4 method for signature 'character,data.frame,character'
readIBSpectra(
                 type, id.file, peaklist.file, annotate.spectra.f =
                 NULL, peaklist.format = NULL, scan.lines = 0,
                 fragment.precision = NULL, fragment.outlier.prob =
                 NULL, ...)

`type`	Name of class of new IBSpectra object: `iTRAQ4plexSpectra`, `iTRAQ8plexSpectra`, `TMT2plexSpectra`, `TMT6plexSpectra`, or `TMT10plexSpectra`
`id.file`	Database search results file in `ibspectra.csv` or `mzIdentML` format. See `identifications.format`. See the vignette for information on converting Mascot dat and Phenyx pidres files into ibspectra format.
`peaklist.file`	Peaklist file, typically in MGF format, see `peaklist.format`. MGF must be centroid!

`mapping.file`	If defined, spectum titles from the peaklist file are linked to the identifications via this file. This can be used when running HCD runs for quantification and CID runs for identification. See Koecher et al., 2009 for details.
`mapping`	Named character vector defining the names of columns in mapping.file. The names must be 'peaklist' and 'id', and the values must correspond to colnames of the mapping files.

`id.file.domap`	When using HCD-CID or a method akin and every spectrum is used for identification, the ID result files of the HCD run can be specfied in `id.file.domap`. Then, the results are merged after mapping the identification results.
`annotate.spectra.f`	Function which changes or annotates the spectra feature data before it is written to IBpectra object. This can be used to calculate and threshold additional scores, for example localization scores of post- translational modifications such as Delta Score (filterSpectraDeltaScore) or PhosphoRS site localization probabilities (annotateSpectraPhosphoRS).
`peaklist.format`	"mgf" (Mascot Generic format) or "mcn" (iTracker Machine Readable output). When NULL, it detects the format on file name extension.
`identifications.format`	"ibspectra.csv" or "mzid" (PSI MzIdentML format). When NULL, file format is guessed based on extension.
`fragment.precision`	Fragment precision for extraction of reporter tags: for each tag and spectrum the m/z-intensity pair with it's mass closest to the known reporter tag mass is extracted within the window true_mass +/- fragment.precision/2.
`fragment.outlier.prob`	Fragment outlier probability filter: After all m/z-intensity pairs have been extracted, those pairs with the fragment.outlier.prob/2 most unprecise m/z values are filtered out.
`decode.titles`	Boolean. Decode spectrum titles in identification file using `URLdecode`. When extracting the DAT file from Mascot web interface, the spectrum titles are encoded - %20 instead of space, etc. Set decode.titles to TRUE to map these titles to the unescaped MGF titles.
`scan.lines`	Read files sequentially scan.lines lines at a time. Can help in case of memory issues, set to 10000 or higher, for example.
`sep`	sep argument of read.table
`...`	Further arguments handed down to `initialize`.

Florian P. Breitwieser, Jacques Colinge

ProteinGroup, IBSpectra, isobar-preprocessing, isobar-analysis, isobar-plots

data(ibspiked_set1)

# get identifier for Ceruplasmin proteins
ceru.acs <- protein.g(proteinGroup(ibspiked_set1),"CERU")
# create a smaller ibspectra w/ only Ceruplasmins
ib.ceru <- subsetIBSpectra(ibspiked_set1,protein=ceru.acs,direction="include")

# write it to a file
tf <- tempfile("isobar")
write.table(as.data.frame(ib.ceru),sep="\t",file=tf,quote=FALSE)

# read it again into an IBSpectra object
ib.ceru2 <- readIBSpectra("iTRAQ4plexSpectra",tf,identifications.format="ibspectra")
ib.ceru2

unlink(tf)

Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Welcome to isobar (v 1.22.0)
   'openVignette("isobar")' and '?isobar' provide help on usage.


Attaching package: 'isobar'

The following object is masked from 'package:BiocGenerics':

    normalize

The following object is masked from 'package:base':

    paste0

Creating ProteinGroup ... done
  reading id file /work/tmp/tmp/Rtmp0vNoqg/isobar1169e0901f3 [type: ibspectra] ... done
 data.frame columns OK
Creating ProteinGroup ... done
iTRAQ4plexSpectra (storageMode: lockedEnvironment)
assayData: 914 features, 4 samples 
  element names: ions, mass 
protocolData: none
phenoData: none
featureData
  featureNames: M261-D01-HS-P1948-1.1658.1658.3.dta.30921
    M261-C08-HS-P1948-1.2302.2302.2.dta.27983 ...
    M261-A09-HS-P1948-1.1155.1155.3.dta.4827 (914 total)
  fvarLabels: peptide modif ... file (12 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
914  spectra
ProteinGroup object
      76 peptides are detected
       3 protein groups with specific peptides