makePeptideSet: peptideSet constructor

Description

This function reads GenePix results (.gpr) files and creates a peptideSet object gathering experiment information.

Usage

makePeptideSet(files = NULL, path = NULL, mapping.file = NULL,
  use.flags = FALSE, rm.control.list = NULL, empty.control.list = NULL,
  bgCorrect.method = "normexp", log = TRUE, check.row.order = FALSE,
  verbose = FALSE)

Arguments

files

A character vector. If NULL, all files with a .gpr extension in the specified path will be read.

path

A character string. The directory where the .gpr files to read are located.

mapping.file

A character string or data.frame. A mapping file that gives information for each sample. See details section below for a list of required fields.

use.flags

A logical. Should spots with flag value -99 or lower be excluded?

rm.control.list

A character vector. The name of the controls to be excluded from the peptideSet.

empty.control.list

A character vector. The name of the empty controls. If non NULL, the intensity of these empty spots will be substracted from remaining intensities.

bgCorrect.method

A character string. The name of the method used for background correction. This is passed to limma's backgroundCorrect method. See details section below and ?backgroundCorrect for more information.

log

A logical. If TRUE, intensities will be log2 transformed after BG correction.

check.row.order

A logical. Should slides be reduced to a common set of peptides?

verbose

A logical. Displays progress and additional information.

Value

A peptideSet object that contain the intensities, peptide sequences and annotations available in the mapping file.

Details

GenePix results files (.gpr) are read when found in either the files or path arguments. By default, the foreground and background median intensities of the "red" channels, "F635 Median" and "B635 Median", are read. The background correction specified in bgCorrect.method is passed to the backgroundCorrect method in the limma package.

The mapping.file can be either a filename or a data.frame. In any case, it should contain at least three columns labeled "filename", "ptid" and "visit". The filenames given here should match those read from the path or files argument, or be a subset of it. For each ptid (patient ID), the visit column should have at least one "pre" and one "post" sample. Any additional column will be kept into the resulting peptideSet and can be used later on for groupping.

If check.row.order = TRUE, the final set of probes is taken to be those with IDs found in all arrays that were read.

Row, Column and Block spatial array position for each probe are stored in the featureRanges slot of the returned object.

Examples

Run this code

# Read gpr files
library(pepDat)
mapFile <- system.file("extdata/mapping.csv", package = "pepDat")
dirToParse <- system.file("extdata/gpr_samples", package = "pepDat")
pSet <- makePeptideSet(files = NULL, path = dirToParse,
                       mapping.file = mapFile, log=TRUE)

# Specify controls to be removed and empty controls
# to be used for background correction.
pSet <- makePeptideSet(files = NULL, path = dirToParse,
                       mapping.file = mapFile, log = TRUE,
                       rm.control.list = c("JPT-control", "Ig", "Cy3"),
                       empty.control.list= c("empty", "blank control"))

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