read.metharray.sheet(base, pattern = "csv$", ignore.case = TRUE, recursive = TRUE, verbose = TRUE)list.fileslist.files?data.frame containing the columns of all the sample sheets.
As described in details, a column named Sentrix_Position is
renamed to Array and Sentrix_ID is renamed to
Slide. In addition the data.frame will contain a column
named Basename.
base (possibly including
subdirectories depending on the argument recursive for
“sample sheet” files (see below). These files are identified
solely on the base of their filename given by the arguments
pattern and ignore.case (note the use of a dollarsign to
mean end of file name). In case multiple sheet files are found, they are all read and the
return object will contain the concatenation of the files.
A sample sheet file is essentially a CSV (comma-separated) file
containing one line per sample, with a number of columns describing
pheno-data or other important information about the sample. The file
may contain a header, in which case it is assumed that all lines up to
and including a line starting with \[Data\] should be dropped.
This is modelled after a sample sheet file Illumina provides. It is
also very similar to the targets file made used by the popular
limma package (see the extensive package vignette).
An attempt at guessing the file path to the IDAT files represented in the sheet is made. This should be doublechecked and might need to manually changed.
The type of methylation array is guess by looking at the number of probes in the IDAT files.
read.metharray.exp and read.metharray for functions
reading IDAT files. list.files for help on the
arguments recursive and ignore.case.
if(require(minfiData)) {
baseDir <- system.file("extdata", package = "minfiData")
sheet <- read.metharray.sheet(baseDir)
}
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