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CopyNumber450kCancer (version 1.0.3)

Baseline Correction for Copy Number Data from Cancer Samples

Description

The 450k arrays are frequently used in the epigenetic studies, the copy number calling from the 450k data is possible but it faces some difficulties in cancer samples regarding the determination of the copy number status due to the false sample centering and baseline shifting. Without solving this issue the CN calling will be inaccurate. CopyNumber450kCancer-package was designed to correct the baseline in cancer samples using the Maximum Density Peak Estimation (MDPE) method. The main advantages for CopyNumber450kCancer-package are: Fast (few seconds per sample), high accuracy rate, in-sample correction, no input parameters needed, low computer sources required, and adaptable for 450k-similar technologies.

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Version

Install

install.packages('CopyNumber450kCancer')

Monthly Downloads

6

Version

1.0.3

License

GPL (>= 2)

Maintainer

Nouraldain Marzouka

Last Published

June 18th, 2015

Functions in CopyNumber450kCancer (1.0.3)

PlotCNV

Plot the CNV Regions with the Density Plot
CopyNumber450kCancer-package

Baseline Correction for Accurate Copy Number Calling in 450k Methylation Array
AutoCorrectPeak

This Function is the Main Function in CopyNumber450kCancer Package Which Correct the Baseline Based on the Density of the Probes/Segments
print.CopyNumber450kCancer_data

Print Function for CopyNumber450kCancer Data(x)
ReadData

Function Reads the Data (i.e. regions file and sample list file) for CopyNumber450kCancer
PlotMerged

To Make Plots with Merged Regions
plotRegions

Genomic Copy Number Plotting Function
ReviewPlot

Interactive Plots for Baseline Correction in Copy Number Data