MSnbase: readMSnSet – R documentation

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readMSnSet

Read 'MSnSet'

Description

This function reads data files to generate an MSnSet instance. It is a wrapper around Biobase's readExpressionSet function with an additional featureDataFile parameter to include feature data. See also readExpressionSet for more details. readMSnSet2 is a simple version that takes a single text spreadsheet as input and extracts the expression data and feature meta-data to create and MSnSet.

Note that when using readMSnSet2, one should not set rownames as additional argument to defined feature names. It is ignored and used to set fnames if not provided otherwise.

Usage

readMSnSet(exprsFile,
           phenoDataFile,
           featureDataFile,
           experimentDataFile,
           notesFile,
           path, annotation,
           exprsArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, ...),
           phenoDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           featureDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           experimentDataArgs = list(sep = sep, header = header, row.names = row.names, quote = quote, stringsAsFactors = stringsAsFactors, ...),
           sep = "\t",
           header = TRUE,
           quote = "",
           stringsAsFactors = FALSE,
           row.names = 1L,
           widget = getOption("BioC")$Base$use.widgets, ...)

readMSnSet2(file, ecol, fnames, ...)

Arguments

Arguments direclty passed to readExpressionSet. The description is from the readExpressionSet documentation page.

`exprsFile`	(character) File or connection from which to read expression values. The file should contain a matrix with rows as features and columns as samples. `read.table` is called with this as its `file` argument and further arguments given by `exprsArgs`.
`phenoDataFile`	(character) File or connection from which to read phenotypic data. `read.AnnotatedDataFrame` is called with this as its `file` argument and further arguments given by `phenoDataArgs`.
`experimentDataFile`	(character) File or connection from which to read experiment data. `read.MIAME` is called with this as its `file` argument and further arguments given by `experimentDataArgs`.
`notesFile`	(character) File or connection from which to read notes; `readLines` is used to input the file.
`path`	(optional) directory in which to find all the above files.
`annotation`	(character) A single character string indicating the annotation associated with this ExpressionSet.
`exprsArgs`	A list of arguments to be used with `read.table` when reading in the expression matrix.
`phenoDataArgs`	A list of arguments to be used (with `read.AnnotatedDataFrame`) when reading the phenotypic data.
`experimentDataArgs`	A list of arguments to be used (with `read.MIAME`) when reading the experiment data.
`sep, header, quote, stringsAsFactors, row.names`	arguments used by the `read.table`-like functions.
`widget`	A boolean value indicating whether widgets can be used. Widgets are NOT yet implemented for `read.AnnotatedDataFrame`.
`...`	Further arguments that can be passed on to the `read.table`-like functions.

Additional argument, specific to readMSnSet:

`featureDataFile`	(character) File or connection from which to read feature data. `read.AnnotatedDataFrame` is called with this as its `file` argument and further arguments given by `phenoDataArgs`.
`featureDataArgs`	A list of arguments to be used (with `read.AnnotatedDataFrame`) when reading the phenotypic data.

Arguments for readMSnSet2:

file

A character indicating the spreadsheet file or a data.frame (new in version 1.19.8). Default, when file is a character, is to read the file as a comma-separated values (csv). If different, use the additional arguments, passed to read.csv, to parametrise file import.

Passing a data.frame can be particularly useful if the spreadsheet is in Excel format. The appropriate sheet can first be read into R as a data.frame using, for example readxl::read_excel, and then pass it to readMSnSet2.

ecol

A numeric indicating the indices of the columns to be used as expression values. Can also be a character indicating the names of the columns. Caution must be taken if the column names are composed of special characters like ( or - that will be converted to a .. If ecol does not match, the error message will dislpay the column names are see by R.

fnames

An optional character or numeric of length 1 indicating the column to be used as feature names.

Value

An instance of the MSnSet class.

Author(s)

Laurent Gatto <lg390@cam.ac.uk>

Examples

## Not run: 
exprsFile <- "path_to_intensity_file.csv"
fdatafile <- "path_to_featuredata_file.csv"
pdatafile <- "path_to_sampledata_file.csv"
## Read ExpressionSet with appropriate parameters
res <- readMSnSet(exprsFile, pdataFile, fdataFile, sep = "\t", header=TRUE)

## End(Not run)

library("pRolocdata")
f0 <- dir(system.file("extdata", package = "pRolocdata"),
          full.names = TRUE,
          pattern = "Dunkley2006")
basename(f0)
res <- readMSnSet2(f0, ecol = 5:20)
res
head(exprs(res)) ## columns 5 to 20
head(fData(res)) ## other columns

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release