read.data.dir {RnBeads} | R Documentation |
Reads in a directory with Illumina Infinium HumanMethylation450 data. The files shoudl be stored as data
read.data.dir(dir, pheno, betas, p.values, bead.counts, sep = rnb.getOption("import.table.separator"), verbose = TRUE)
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 |
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. |
Colnames in all files should match. They will be returned as the samples element of the list.
Object of type RnBeadSet
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Pavlo Lutsik