read.celfiles {oligo} | R Documentation |
Parser to CEL files
Description
Reads CEL files.
Usage
read.celfiles(..., filenames, pkgname, phenoData, featureData,
experimentData, notes, verbose = TRUE, sampleNames, rm.mask = FALSE,
rm.outliers = FALSE, rm.extra = FALSE, sd = FALSE, checkType = TRUE,
useAffyio = TRUE)
read.celfiles2(channel1, channel2, pkgname, phenoData, featureData,
experimentData, notes, verbose = TRUE, sampleNames, rm.mask = FALSE,
rm.outliers = FALSE, rm.extra = FALSE, sd = FALSE, checkType = TRUE,
useAffyio = TRUE)
Arguments
... |
names of files to be read. |
filenames |
a character vector with the CEL filenames. |
channel1 |
a character vector with the CEL filenames for
the first 'channel' on a Tiling application |
channel2 |
a character vector with the CEL filenames for
the second 'channel' on a Tiling application |
pkgname |
alternative data package to be loaded. |
phenoData |
phenoData |
featureData |
featureData |
experimentData |
experimentData |
notes |
notes |
verbose |
logical |
sampleNames |
character vector with sample names (usually
better descriptors than the filenames) |
rm.mask |
logical . Read masked? |
rm.outliers |
logical . Remove outliers? |
rm.extra |
logical . Remove extra? |
sd |
logical . Read SD? |
checkType |
logical . Check type of each file? This can be
time consuming. |
useAffyio |
logical . Use 'affyio' instead of 'affxparser'
to read in CEL files. |
Details
When using 'affyio' to read in CEL files, the user can read compressed
CEL files (CEL.gz). Additionally, 'affyio' is much faster than 'affxparser'.
Value
ExpressionFeatureSet
|
if Expresssion arrays |
ExonFeatureSet
|
if Exon arrays |
SnpFeatureSet
|
if SNP arrays |
TilingFeatureSet
|
if Tiling arrays |
See Also
list.celfiles
, read.xysfiles
Examples
if(require(pd.mapping50k.xba240) & require(hapmap100kxba)){
celPath <- system.file("celFiles", package="hapmap100kxba")
celFiles <- list.celfiles(celPath, full.name=TRUE)
affySnpFeatureSet <- read.celfiles(celFiles)
}
[Package
oligo version 1.8.3
Index]