Description Usage Arguments Examples
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 | Sample name |
Chromosome | Chromosome number chr1, chr2, ....., chrX, chrY |
bp.Start | number, start point for the segment |
bp.End | end point for the segment |
Num.of.Markers | Number of the probes or markers in the segment |
Mean | is the log value for the segment (the mean of the log values for all the probes in the segment, it is the same value that is used in CopyNumber450k package) |
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) |
1 |
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. |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #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
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