Description Objects from the Class Slots Methods Author(s) References
Objects of this class hold data used by the readDepth package, including input parameters, depth-of-coverage values, entrypoint information, etc.
Objects can be created by calls of the form new("rdObject")
.
In order to successfully create this class, you'll need to have the proper directory structure set up. See the readDepth documentation for details (http://github.com/chrisamiller/readDepth)
params
:Object of class "numeric"
a named list containing input parameters
binParams
:Object of class "data.frame"
a data frame that contains calculated values, like thresholds,
mean # of reads per bin, ploidy calculations, etc.
entrypoints
:Object of class "data.frame"
a data frame containing the entrypoints and mapability values
readInfo
:Object of class "data.frame"
a data frame containing information on the input data (reads)
chrs
:Object of class "list"
a named list with each slot containing a dataframe that holds
a given chromosome's read depth, gc content, and mapability
for each bin.
No methods defined with class "rdObject" in the signature.
Chris Miller (chrisamiller@gmail.com)
readDepth: a parallel R package for detecting copy-number alterations from short sequencing reads (in preparation)
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