read.idat.files2 {RnBeads} | R Documentation

## read.idat.files2

### Description

Reads a directory of `.idat` files and initializes an object of type `MethyLumiSet`.

### Usage

    read.idat.files2(base.dir, barcodes = NULL, sample.sheet = NULL,
      sep.samples = rnb.getOption("import.table.separator"), load.chunk = NULL,
      keep.methylumi = FALSE, verbose = TRUE)

### Arguments

`base.dir` | Directory that contains the `.idat` files to be read; or a character vector of such directories.
`barcodes` | Optional non-empty `character` vector listing the barcodes of the samples that should be loaded. If supplied, this vector must not contain `NA` among its elements.
`sample.sheet` | Optional file name containing a table of sample annotation data, or the table itself in the form of a `data.frame` or `matrix`. Only (and all) samples defined in this table will be loaded. The table is expected to contain a column named `"barcode"` that lists the samples' Sentrix barcodes. If such a column is not present, this function searches for columns `"Sentrix_ID"` and `"Sentrix_Position"` (or similar) that build a barcode.
`sep.samples` | character used as field separator in the sample sheet file. Default value is taken by the call to `rnb.getOption("import.table.separator")`
`load.chunk` | `integer` of size one, giving the number of IDAT files which should be loaded in one loading cycle or `NULL`, in which case an attempt will be made to load all files in one go. Should be assigned in case the number of IDATs is more than one thousand.
`keep.methylumi` | a flag indicating whether the a `MethyLumiSet` object should be returned instead of a `RnBeadRawSet`.
`verbose` | Flag indicating ifthe messages to the logger should be sent. Note that the logger must be initialized prior to calling this function. Logging is useful for keeping a record of the downloaded and processed samples. Also, informative messages are stored in case of an error.

### Details

If neither `barcodes`, nor `sample.sheet` are specified, the function attempts to locate a file in `base.dir` containing sample annotation information. It fails ifsuch a file cannot be (unambiguously) identified. If both `barcodes` and `sample.sheet` are supplied, only `sample.sheet` is used in loading methylation data. The value of `barcodes` is tested for validity but it is not used as a filter.

### Value

Loaded dataset of HumanMethylation450K samples, encapsulated in an object of type `MethyLumiSet`.

### Author(s)

Pavlo Lutsik

### See Also

`methylumIDAT` in package methylumi

[Package RnBeads version 1.10.8 Index]