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.
|Author||Nour-al-dain Marzouka [aut, cre]|
|Date of publication||2015-08-20 19:23:59|
|Maintainer||Nour-al-dain Marzouka <email@example.com>|
|License||GPL (>= 2)|
AutoCorrectPeak: This Function is the Main Function in CopyNumber450kCancer...
CopyNumber450kCancer-package: Baseline Correction for Accurate Copy Number Calling in 450k...
PlotCNV: Plot the CNV Regions with the Density Plot
PlotMerged: To Make Plots with Merged Regions
plotRegions: Genomic Copy Number Plotting Function
print.CopyNumber450kCancer_data: Print Function for CopyNumber450kCancer Data(x)
ReadData: Function Reads the Data (i.e. regions file and sample list...
ReviewPlot: Interactive Plots for Baseline Correction in Copy Number Data