CopyNumber450kCancer (version 1.0.3)

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

Description

The input should be two files regions file and sample list file. regions file: contains the data for all the regions/segments in all the sample sample list file: contains the number of the samples, the names of the samples and user comment. The header of the segments/regions file should be in this order and with these names: "Sample", "Chromosome", "bp.Start", "bp.End", "Num.of.Markers", "Mean" The segments file should have all the samples in one file Be carful for the dots and it is case sensitive. Sample: the sample name Chromosome: the chromosome number chr1, chr2, ....., chrX, chrY bp.Start: number, the start point for the segment bp.End: number, the end point for the segment Num.of.Markers: Mean: is the log value for the segment The header of the sample list file should be in this order and with these names: To check if the header of the sample list file is ok "Number", "Sample", "Comment" Be carful it is case sensitive. Number: is the number of the sample 1,2,3,.... Sample: the name of the samples Comment: any comment the user want to see in the reviewing step and in the QC file, ex karyotyping.

Usage

ReadData(regions_file, Sample_list, copynumber450k = F)

Arguments

regions_file

The segmentaion file (CSV file)

Sample_list

The CSV file that contains the names of the samples and the user comments

copynumber450k

True if the file is the output of copynumber450k, defualt is FALSE.

Examples

#example
# the package contains example files: regions.csv and sample_list.csv
#to load the example regions.csv and sample_list.csv files
regions <- system.file("extdata", "regions.csv", package="CopyNumber450kCancer")
sample_list <- system.file("extdata", "sample_list.csv", package="CopyNumber450kCancer")

# Creat the object for the package
object <- ReadData(regions,sample_list) 

# Baseline autocorrection, 
# this will creat different plot and QC and new regions file in the working directory
object <- AutoCorrectPeak(object)

# For manual revision and manual baseline determination
# object <- ReviewPlot(object)

# To plot the final plots
PlotCNV(object) # to plot all the samples
PlotCNV(object, select= c(1,4), comment=FALSE, cutoff=0.1, markers=20) # to plot some samples