sean-cho/epicopy

Epicopy R package for CNV identification from methylation microarrays.

Epicopy

Epicopy is an R package that obtains copy number variation (CNV) information from Illumina Human Methylation 450K microarrays. If the users have their own reference normal samples or decide to not use any normals for reference (see Usage section below), Epicopy can be used as a standalone package.

If not, users may choose to install its companion package "EpicopyData" which contains a series of normal tissues compiled from the Cancer Genome Atlas (TCGA) effort. It contains normal tissues from three sources; thyroid, breast, and lung. For more information on EpicopyData please visit the EpicopyData page.

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Changelog

[20170202] v0.99.7: Remove EpicopyData dependency for vignette.

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Installation

The preferred method for installation is through Hadley Wickham's install_github function through the package devtools.

If users have their own normal samples, it is recommended that they install the standalone version as it is much smaller in size.

Standalone

To install the standalone package use the following line:

devtools::install_github('sean-cho/Epicopy')

Complete

The complete version includes all the normals compiled from TCGA.

Step 1: Install EpicopyData

Please download the binary release here and run the following lines of code.

path <- "path.to.file/EpicopyData_1.0.1.tar.gz"
install.packages(path, repos = NULL, type = 'source')

Step 2a: Install Epicopy without vignette

devtools::install_github('sean-cho/Epicopy')

Step 2b: Install Epicopy with vignette

Warning: Please note that the vignette includes the complete processing of three example raw data files and may take a while to build.

devtools::install_github('sean-cho/Epicopy', build_vignette = TRUE)

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Usage

Standalone

Since no vignette is built, users can view the online vignette for examples here. Additional information is also available in the help files.

The key to using Epicopy as a standalone package is to specify normals in the samplesheet or, missing that, Epicopy will use the median of all the samples in the epicopy or getLRR functions. This is important, as the default argument uses all normals included in the EpicopyData package.

With EpicopyData normals

Install and build the vignette. Users may specify any of the normals included in with the EpicopyData package using the options:

• all or NULL (default): Uses all EpicopyData normals, or median of all samples if EpicopyData is not installed.
• thyroid, breast, or lung: Uses normal tissue of specified organ.

More information is available using ?getLRR.

epicopy's Issues

Error in getLRR function

Hi,

I have just installed Epicopy and EpicopyData packages, but I get an error in getLRR function.
I tried first with Normals samples in Epicopy package

epi_lrr <- getLRR(rgSet = RGset_tumor, Normals = NA, Ref = 'median')

and then pre-processing Normal samples from minfiData package and creating a second RGset object related to these Normal samples.

epi_lrr <- getLRR(rgSet = RGset_tumor, Normals = RGset_normal, Ref = 'median')

But I got same error in both cases

"Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘pData<-’ for signature ‘"RGChannelSet", "data.frame"’

Do you know how to fix this this problem?
Thank you very much in advance
Best regards,
Jacob