pep.massmatch: Mass match a vector of masses to a database.

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.massmatch(input, db, presetdb = NA, dbpath = NA, dbseparator = ",",
  dbheader = FALSE, ID_thresh = 10, masscorrection = F, FDR = F,
  iterations = 10, checkdb = F, graphics = F, verbose = F)

Arguments

input	Numeric. Either a single value, a vector of values, or a dataframe or matrix with one column with name MW
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
ID_thresh	Numeric. Maximal allowed mass difference in ppm for identification.
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.
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 pep_massmatched that can be used for subsequent analysis using labelpepmatch functions.

Author(s)

Rik Verdonck & Gerben Menschaert

See Also

pep.id, pep.massmatch

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