read.metharray.sheet {minfi} | R Documentation

## Reading an Illumina methylation sample sheet

### Description

Reading an Illumina methylation sample sheet, containing pheno-data information for the samples in an experiment.

### Usage

    read.metharray.sheet(base, pattern = "csv$", ignore.case = TRUE,
        recursive = TRUE, verbose = TRUE)

### Arguments

`base` | The base directory from which the search is started.
`pattern` | What pattern is used to identify a sample sheet file, see `list.files`
`ignore.case` | Should the file search be case sensitive?
`recursive` | Should the file search be recursive, see `list.files`?
`verbose` | Should the function be verbose?

### Details

This function search the directory `base` (possibly including subdirectories depending on the argument `recursive` for “sample sheet” files (see below). These files are identified solely on the base of their filename given by the arguments `pattern` and `ignore.case` (note the use of a dollarsign to mean end of file name).

In case multiple sheet files are found, they are all read and the return object will contain the concatenation of the files.

A sample sheet file is essentially a CSV (comma-separated) file containing one line per sample, with a number of columns describing pheno-data or other important information about the sample. The file may contain a header, in which case it is assumed that all lines up to and including a line starting with `\[Data\]` should be dropped. This is modelled after a sample sheet file Illumina provides. It is also very similar to the `targets` file made used by the popular `limma` package (see the extensive package vignette).

An attempt at guessing the file path to the IDAT files represented in the sheet is made. This should be doublechecked and might need to manually changed.

The type of methylation array is guess by looking at the number of probes in the IDAT files.

### Value

A `data.frame` containing the columns of all the sample sheets. As described in details, a column named `Sentrix_Position` is renamed to `Array` and `Sentrix_ID` is renamed to `Slide`. In addition the `data.frame` will contain a column named `Basename`.

### Author(s)

Kasper Daniel Hansenkhansen@jhsph.edu.

### See Also

`read.metharray.exp` and `read.metharray` for functions reading IDAT files. `list.files` for help on the arguments `recursive` and `ignore.case`.

### Examples

    if(require(minfiData)) {

    baseDir <- system.file("extdata", package = "minfiData")
    sheet <- read.metharray.sheet(baseDir)

    }

[Package minfi version 1.34.0 Index]