Description Creating Objects Slots Methods Author(s) See Also Examples
Container for data from high-throughput assays mapped to chromosome locations.
The most convenient way to create a ChrStrandData object is to use the
makeChrStrandData
function, which can be used to convert data
stored in either an ExpressionSet
or data frame into a
ChrStrandData
object:
makeChrStrandData(ALL, lib = "hgu95av2.db")
a 'list', whose components correspond to samples in the same order as appearing in the columns of 'expr'. Each component is also a 'list', named by chromosomes "1"-"22", "X" and "Y". Each named component is again a 'list' with two elements named "posS" and "negS", corresponding to the forward and reverse strands of a chromosome, each of which is a list containing start coordinates ("x"), end coordinates("xe") and the corresponding data values ("y").
A string giving the name of the annotation data package to use.
The list of chromosomes represented in the object.
Class-specific methods.
annotation(ChrStrandData)
Returns the name of the AnnotationDbi library used to annotate the object.
chrNames(ChrStrandData)
Returns a list of the chromosomes represented in the object.
sampleNames(ChrStrandData)
Returns the names of the samples associated with the object.
Standard generic methods:
show(ChrStrandData)
Generates a short description of the ChrStrandData object.
summary(ChrStrandData)
Generates a summary of the data available for each chromosome in the ChrStrandData object.
Tim F Rayner
makeChrStrandData
, ChrStrandMatrix-class
.
1 2 | data('demo')
chrdata <- makeChrStrandData(exprs(ALLs.chr22), lib = "hgu95av2.db")
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