read.data.dir: read.data.dir

In RnBeads: RnBeads

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

RnBeads documentation built on March 3, 2021, 2 a.m.