CopyNumber450kCancer: Baseline Correction for Copy Number Data from Cancer Samples

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 <nour.marzouka@medsci.uu.se>
License
GPL (>= 2)
Version
1.0.4

View on CRAN

Man pages

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

Files in this package

CopyNumber450kCancer
CopyNumber450kCancer/inst
CopyNumber450kCancer/inst/extdata
CopyNumber450kCancer/inst/extdata/regions.csv
CopyNumber450kCancer/inst/extdata/sample_list.csv
CopyNumber450kCancer/NAMESPACE
CopyNumber450kCancer/R
CopyNumber450kCancer/R/CopyNumber450kCancer.R
CopyNumber450kCancer/vignettes
CopyNumber450kCancer/vignettes/CopyNumber450kCancer.pdf
CopyNumber450kCancer/MD5
CopyNumber450kCancer/DESCRIPTION
CopyNumber450kCancer/man
CopyNumber450kCancer/man/PlotMerged.Rd
CopyNumber450kCancer/man/PlotCNV.Rd
CopyNumber450kCancer/man/ReviewPlot.Rd
CopyNumber450kCancer/man/AutoCorrectPeak.Rd
CopyNumber450kCancer/man/print.CopyNumber450kCancer_data.Rd
CopyNumber450kCancer/man/CopyNumber450kCancer-package.Rd
CopyNumber450kCancer/man/ReadData.Rd
CopyNumber450kCancer/man/plotRegions.Rd