read.data.dir {RnBeads} | R Documentation

## read.data.dir

### Description

Reads in a directory with Illumina Infinium HumanMethylation450 data. The files shoudl be stored as data

### Usage

    read.data.dir(
      dir,
      pheno,
      betas,
      p.values,
      bead.counts,
      sep = rnb.getOption("import.table.separator"),
      verbose = TRUE
    )

### Arguments

`dir` | directory containing the table files
`pheno` | a file containing data sample annotations and phenotypic information
`betas` | a file containing the beta values. If not supplied, the routine will look in dir for a file containing "beta" token in the filename
`p.values` | a file containing the detection p values. If not supplied, the routine will look in dir for a file containing "pval" token in the filename
`bead.counts` | a file containing the bead counts (optional). If not supplied, the routine will look in dir for a file containing "bead" token in the filename
`sep` | character used as field separator in the tables files. Default value is taken by the call to `rnb.getOption("import.table.separator")`
`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

Colnames in all files should match. They will be returned as the samples element of the list.

### Value

Object of type `RnBeadSet`.

### Author(s)

Pavlo Lutsik

[Package RnBeads version 2.12.2 Index]