writeMSF: writeMSF.

Description Usage Arguments Details Value

Description

Write a spectrum file in MSFinder format.

Usage

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writeMSF(x, ...)

## Default S3 method:
writeMSF(x, precursormz, precursortype = "[M+H]+",
  name = "unknown", ionmode = "Positive", ms1spec = NULL,
  retentiontime = NULL, outfile = NULL, ...)

## S3 method for class 'findMAIN'
writeMSF(x, rank = 1, ms2spec = NULL, outfile = NULL,
  ...)

Arguments

x

A matrix, 'findMAIN' or other object for which methods are defined.

...

Arguments passed to method writeMSF.findMAIN.

precursormz

Precursor m/z

precursortype

Precursor type

name

Give the spectrum a name

ionmode

"Positive" or "Negative"

ms1spec

(Optional) MS1 spectrum.

retentiontime

(Optional) retention time of the spectrum that will be used by MSFINDER for refined prediction.

outfile

Name of MAT file, or NULL for 'stdout'.

rank

Which rank from 'findMAIN' should be exported

ms2spec

If available you may provide the according MS2 spectrum

Details

In the default case 'x' can be a matrix or data frame, where the first two columns are assumed to contain the 'mz' and 'intensity' values, respectively. Further arguments 'precursormz' and 'precursortype' are required in this case. Otherwise 'x' can be of class findMAIN.

Value

Write spectrum to MAT file for evaluation in MSFINDER.


InterpretMSSpectrum documentation built on May 2, 2019, 11:05 a.m.