pep.id: Mass match peak pairs from a pepmatched object.

In goat-anti-rabbit/labelpepmatch.R: Tools For Interpreting Mass Spectra With Labeled Peptides

Description

Mass match peak pairs from a pepmatched object to known databases. Can call inbuilt databases, but you can also use your own local database.

Usage

pep.id(pepmatched, ID_thresh = 10, db, presetdb = NA, dbpath = NA,
  dbseparator = ",", dbheader = FALSE, masscorrection = FALSE,
  cores = 1, FDR = TRUE, iterations = 100, checkdb = F, graphics = F,
  verbose = FALSE)

Arguments

pepmatched	Input object of class pepmatched, generated by the pepmatch() function of this package.
ID_thresh	Numeric. Maximal allowed mass difference in ppm for identification.
db	In case no preset database is chosen: a database (table) with the first 3 columns "name","MW" and "sequence" (as read in with the download_lpm_db function) The amino acid sequences have to obey rules when you want to use them for mass recalculation or generation of a decoy database. Amino acids have to be capitalized one letter codes. For details, see calculate_peptide_mass
presetdb	A preset database. For the future (not ready yet)
dbpath	Character. In case a local database is used. Should be the filepath of a table, separated by dbseparator, with first tree columns: name, mass in Dalton and sequence.
dbseparator	Character. Column separator of database.
dbheader	Logical. Does the database have a header? Default FALSE
masscorrection	Logical. Should masses be corrected on the basis of identifications? Caution should be payed here, since this will only work with a sufficiently high number of real matches. This rather sketchy feature should be considered something interesting to have a look at, rather than a compulsory part of the pipeline. Always also run without mass correction and compare! Default is FALSE.
cores	Interger. Number of cores that can be used on the computer for calculation. When >1, the packages foreach and doParallel will be used for multithreading.
FDR	Logical. Test false discovery rate of peptide mass match identification by calculating a decoy database and look how many hits you get there. Uses generate_random_db.
iterations	How many iterations of FDR should be ran? This might take some time for larger datasets.
checkdb	Look if the masses and sequences in your database make sense. UNDER CONSTRUCTION!!!
graphics	Only applies when FDR is TRUE.
verbose	Logical. If TRUE, verbose output is generated during identifications.

Value

An object of class pepmatched with added mass matches that can be used for subsequent analysis using labelpepmatch functions. This pepmatched object will also contain a couple of extras like detailed pep.id parameters, details about the FDR estimation, a list of identified peptides with their counts, and a deltavector with the mass shifts in case the mass correction has been applied.

Author(s)

Rik Verdonck & Gerben Menschaert

See Also

generate_random_db, pep.massmatch

goat-anti-rabbit/labelpepmatch.R documentation built on May 17, 2019, 7:29 a.m.