RnBeads (version 1.4.0)

read.data.dir: 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.

Value

Object of type RnBeadSet.

Details

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