rnb.execute.import: rnb.execute.import

In RnBeads: RnBeads

Description

Loads the data from the specified type and encapsulates it in either an RnBSet-inheriting object

Usage

rnb.execute.import(
  data.source,
  data.type = rnb.getOption("import.default.data.type"),
  dry.run = FALSE,
  verbose = TRUE
)

Arguments

data.source	non-empty character vector or list specifying the location of the data items. The expected format depends on the data.type that is given. See the Details section.
data.type	type of the input data; must be one of "idat.dir", "data.dir", "data.files", "GS.report", "GEO" or "rnb.set".
dry.run	if TRUE and data.type is "bs.bed.dir", only a test data import is performed and first 10,000 lines are read from each BED file
verbose	flag specifying whether diagnostic output should be written to the console or to the RnBeads logger in case the latter is initialized

Details

The interpretation of data.source depends on the value of data.type and is summarized in the following table:

data.type	Type of data.source	Maximal length of data.source	Interpretation
"infinium.idat.dir"	list or character	2	(1) Directory containing IDAT files; (2) a sample annotation table as a data.frame or the name of the corresponding file
"infinium.data.dir"	character	1	Directory containing data tables in plain text format. The directory should contain one file with Sample|sample token in the filename for the table of sample annotations, and one file with a token beta in the filename, with beta-values. It may also contain tables with p-values (token pval) and bead counts (bead). In the latter case beta-value, p-value and bead count tables should have matching columns and rows. The beta-value, p-value and bead-count tables should contain row names, i.e. the first column should contain the Infinium CG identifiers and not have a column header (for that the first row should have one entry less than all other rows). Sample annotation table should contain as many rows as there are columns in other tables. The character used as value separator in the text tables can be set using the import.table.separator option (see rnb.options for details).
"infinium.data.files"	character	2..4	The character vector should contain at least full paths to the sample annotation file and beta-value table. Detection p-values and bead counts table can be added as the third and the fourth elements. The table format requirements are the same as for "data.dir" above.
"infinium.GS.report"	character	1	Genome Studio report file
"infinium.GEO"	character	1	GEO identifier or downloaded series matrix file
"bs.bed.dir"	list or character	1..3	(1) Directory with BED files each giving a DNA methylation profile of a sample; (2) a sample annotation table as a data.frame or the name of the corresponding file; (3) number of the sample annotation sheet column containing the file names. One of the first two elements have to be present. In case only the directory is specified, it should contain a sample annotation file with a token "sample" in the file name. In case only the sample sheet is specified, one column should be giving full absolute paths of the BED-like files with sequencing information. If both elements (1) and (2) are specified, the files should reside in the directory, specified as element (1). If the third element is absent, an attempt will be made to find the file name containing column automatically. For this reason the file names in the sample annotation sheet should be given with extensions (".bed", ".cov" etc).
"rnb.set"	RnBSet	1	object of class inheriting from RnBSet

Value

Loaded data as an object of type RnBSet (when the input data type is "data.dir", "data.files" or "GEO") or of type MethyLumiSet (when the data type is "idat.dir" or "GS.report").

Author(s)

Pavlo Lutsik

See Also

read.data.dir, read.idat.files, read.GS.report, rnb.read.geo, read.bed.files #'

Examples

# Directory where your data is located
data.dir <- "~/RnBeads/data/Ziller2011_PLoSGen_450K"
idat.dir <- file.path(data.dir, "idat")
sample.annotation <- file.path(data.dir, "sample_annotation.csv")
data.source <- c(idat.dir, sample.annotation)
rnb.set <- rnb.execute.import(data.source = data.source, data.type = "idat.dir")

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