rdObject-class: Class "rdObject" ~~~

In chrisamiller/copyCat: Find regions of genomic copy number loss and gain from short reads

Description

Objects of this class hold data used by the readDepth package, including input parameters, depth-of-coverage values, entrypoint information, etc.

Objects from the Class

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://code.google.com/p/readdepth)

Slots

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.

Methods

No methods defined with class "rdObject" in the signature.

Author(s)

Chris Miller ([e-mail])

References

readDepth: a parallel R package for detecting copy-number alterations from short sequencing reads (in preparation)

chrisamiller/copyCat documentation built on July 20, 2021, 12:59 a.m.