cnSegCallingProcess {MPAgenomics} | R Documentation |
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.
cnSegCallingProcess(dataSetName, normalTumorArray, chromosome = 1:22, method = c("PELT", "cghseg"), Rho = NULL, Kmax = 10, listOfFiles = NULL, onlySNP = TRUE, savePlot = TRUE, nclass = 3, cellularity = 1, ...)
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. |
method |
method of segmentation, either "PELT" or "cghseg". |
Rho |
For method="PELT", vector containing all the penalization values to test for the segmentation. If no values are provided, default values will be used. |
Kmax |
For method="cghseg", maximal number of segments. |
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
#DO NOT EXECUTE before reading the vignette # seg1=cnSegCallingProcess("data1",normalTumorArray,chromosome=20:21) # seg2=cnSegCallingProcess("data2",chromosome=20:21)