isobar-import: Loading data into IBSpectra objects using readIBSpectra

In fbreitwieser/isobar: Analysis and quantitation of isobarically tagged MSMS proteomics data

Description

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.

Usage

## 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, ...)

Arguments

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.

Author(s)

Florian P. Breitwieser, Jacques Colinge

See Also

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

Examples

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)

fbreitwieser/isobar documentation built on May 16, 2019, 12:01 p.m.