read.idat: Read Illumina expression data from IDAT files

In hdeberg/limma: Linear Models for Microarray Data

Description

Read Illumina BeadArray data from IDAT and manifest (.bgx) files for gene expression platforms.

Usage

read.idat(idatfiles, bgxfile, path = NULL, bgxpath = path,
          dateinfo = FALSE, annotation = "Symbol", tolerance = 0, verbose = TRUE)

Arguments

idatfiles	character vector specifying the IDAT files to be read in. Gzipped files are not accepted.
bgxfile	character string specifying bead manifest file (.bgx) to be read in. May be gzipped.
path	character string giving the directory containing the IDAT files. The default is the current working directory.
bgxpath	character string giving the directory containing the bgx manifest file. Defaults to the same directory as for IDAT files.
dateinfo	logical. Should date and software version information be read in?
annotation	character vector of annotation columns to be read from the manifest file.
tolerance	integer. The number of probe ID discrepancies allowed between the manifest and any of the IDAT files.
verbose	logical. Should progress messages are sent to standard output?

Details

Illumina's BeadScan/iScan software outputs probe intensities in IDAT format (encrypted XML files) and uses probe information stored in a platform specific manifest file (.bgx). These files can be processed using the low-level functions readIDAT and readBGX from the illuminaio package (Smith et al, 2013).

The read.idat function provides a convenient way to read these files into R and to store them in an EListRaw-class object. The function serves a similar purpose to read.ilmn, which reads text files exported by Illumina's GenomeStudio software, but it reads the IDAT files directly without any need to convert them first to text.

The function reads information on control probes as well for regular probes. Probe types are indicated in the Status column of the genes component of the EListRaw object.

The annotation argument specifies probe annotation columns to be extracted from the manifest file. The manifest typically contains the following columns: Species, Source, Search_Key, Transcript, ILMN_Gene, Source_Reference_ID, RefSeq_ID, Unigene_ID, Entrez_Gene_ID, GI, Accession, Symbol, Protein_Product, Probe_Id, Array_Address_Id, Probe_Type, Probe_Start, Probe_Sequence, Chromosome, Probe_Chr_Orientation, Probe_Coordinates, Cytoband, Definition, Ontology_Component, Ontology_Process, Ontology_Function, Synonyms, Obsolete_Probe_Id. Note that the Probe_Id and Array_Address_Id columns are always read and do not need to included in the annotation argument.

If more than tolerance probes in the manifest cannot be found in an IDAT file then the function will return an error.

Value

An EListRaw object with the following components:

E	numeric matrix of raw intensities.
other$NumBeads	numeric matrix of same dimensions as E giving number of beads used for each intensity value.
other$STDEV	numeric matrix of same dimensions as E giving bead-level standard deviation or standard error for each intensity value.
genes	data.frame of probe annotation. This includes the Probe_Id and Array_Address_Id columns extracted from the manifest file, plus a Status column identifying control probes, plus any other columns specified by annotation.
targets	data.frame of sample information. This includes the IDAT file names plus other columns if dateinfo=TRUE.

Author(s)

Matt Ritchie and Gordon Smyth

References

Smith ML, Baggerly KA, Bengtsson H, Ritchie ME, Hansen KD (2013). illuminaio: An open source IDAT parsing tool. F1000 Research 2, 264. doi: 10.12688/f1000research.2-264.v1

See Also

read.ilmn imports gene expression data as a text file exported from GenomeStudio.

neqc performs normexp by control background correction, log transformation and quantile between-array normalization for Illumina expression data.

propexpr estimates the proportion of expressed probes in a microarray.

detectionPValues computes detection p-values from the negative controls.

Examples

## Not run: 
idatfiles <- dir(pattern="idat")
bgxfile <- dir(pattern="bgx")
x <- read.idat(idatfiles, bgxfile)
x$other$Detection <- detectionPValues(x)
propexpr(data)
y <- neqc(data)

## End(Not run)

hdeberg/limma documentation built on Dec. 20, 2021, 3:43 p.m.