read.progenesis: Read progenesis data.

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

Description

Read in data generated with progenesis LC-MS. Use the standard output function in progenesis and write your file to a table or csv. Do not bother about extra statistics columns. Normalizing the data is not neccesary.

Usage

read.progenesis(indata = file.choose(), designvector, samplenames = NA,
  sep = ",", dec = ".", intORabu = "int", chargename = "Charge",
  abundname = "Raw abundance", intensname = "Intensity",
  rettimename = "Sample retention time (min)", verbose = FALSE)

Arguments

indata	Character. A table exported from progenesis LC-MS. Either reads a filepath, or reads the file directly if you are in the right folder. If no indata is specified, a prompt is presented.
designvector	Character. A Character vector of length N + 2 with N = number of runs. A vector with the design of the labelling. This is a vector that contains in this exact order: name of first condition, name of second condition, labelling order of first sample, labelling order of second sample, ... labelling order of last sample. The labelling order can either be F (forward, first condition is light), or R (reverse, first condition is heavy).
samplenames	Character. A character vector with the names of your samples. The length should be the number of runs.
sep	Character. The field separator of the data you read in. Default is ","
dec	Character. The decimal separator of the data you read in. Default is "."
intORabu	Character. Can be "int" or "abu", default "int". Will you work with the intensity (height of the peaks) or the abundance (surface under the peaks) of the data?
chargename	Character. Name of the charge columns. Default is Charge
abundname	Character. Name of abundance columns header. Default is Raw abundance
intensname	Character. Name of intensity columns header. Default is Intensity
rettimename	Character. Name of retention time columns header. Default is Sample retention time (min)
verbose	Logical. Gives verbose output.

Value

An object of class lpm_input that that can be used for subsequent analysis using labelpepmatch functions. Feeds straigth in the pepmatch function.

Author(s)

Rik Verdonck & Gerben Menschaert

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