Description Usage Arguments Value Author(s) Examples
This function applies the PELT method to segment each signal of the dataset and launches CGHcall for calling segments and detect aberrations. Results will be stored in a text file in the segmentation folder of the aroma architecture.
1 2 3 4 5 6 7 8 9 10 11 12 |
dataSetName |
name of the data-set folder in the rawData folder containing the signals to use. |
normalTumorArray |
Only in the case of normal-tumor study. A csv file or a data.frame containing the mapping between normal and tumor files. The first column contains the name of normal files and the second the names of associated tumor files. |
chromosome |
A vector containing the chromosomes to segment. |
Rho |
A Vector containing all the penalization values to test for the segmentation. If no values are provided, default values will be used. |
listOfFiles |
A vector containing the names of the files from the dataSetName to use. |
onlySNP |
If TRUE, only the SNP probes will be used. |
savePlot |
If TRUE, save the segmented signal in figures folder. |
nclass |
The number of levels to be used for calling. Either 3 (loss, normal, gain), 4 (including amplifications), 5 (including double deletions) (default=3). |
cellularity |
Percentage of tumored cells in the sample (default=1). |
... |
Other parameters of CGHcall function |
a data.frame containg columns :
Name of the file.
The chromosome of the segment.
The starting position (in bp) of a segment. This position is not included in the segment.
The ending position (in bp) of a segment.This position is included in the segment.
Number of probes in the segment.
Mean of the segment.
The calling of segment ("double loss", "loss", "normal", "gain" or "amplification").
Quentin Grimonprez
1 2 3 4 5 6 | ## Not run:
#DO NOT EXECUTE before reading the vignette
seg1=cnSegCallingProcess("data1",normalTumorArray,chromosome=20:21)
seg2=cnSegCallingProcess("data2",chromosome=20:21)
## End(Not run)
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