read.idat(idatfiles, bgxfile, dateinfo = FALSE, annotation = "Symbol", tolerance = 0L, verbose = TRUE)
EListRaw
object with the following components:
E
giving number of beads used for each intensity value.E
giving bead-level standard deviation or standard error for each intensity value.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
.dateinfo=TRUE
.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 "Probe_Id"
and "Array_Address_Id"
are always extracted 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.
read.ilmn
imports gene expression data output by 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.
## 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)
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