readMSnSet {MSnbase} | R Documentation

## 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>

### See Also

The `grepEcols` and `getEcols` helper functions to identify the `ecol` values. The `MSnbase-io` vignette illustrates these functions in detail. It can be accessed with `vignette("MSnbase-io")`.

### 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

[Package MSnbase version 2.20.1 Index]