segFracBSignal {MPAgenomics} | R Documentation |
This function launches the segmentation of allele B fraction only for heterozygous SNPs.
segFracBSignal(dataSetName, normalTumorArray, chromosome = 1:22, method = c("PELT", "cghseg"), Rho = NULL, Kmax = 10, listOfFiles = NULL, savePlot = TRUE, verbose = TRUE)
dataSetName |
The name of the data-set folder (it must correspond to a folder name in rawData folder.). |
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 with the chromosomes to be segmented. |
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 in dataSetName folder for which the allele B profile is segmented (default is all the files). |
savePlot |
if TRUE, graphics of the segmented allele B profile will be saved in the figures/dataSetName/segmentation/fracB folder. (default=TRUE). |
verbose |
if TRUE print some informations |
a data.frame where each row correspond to a different segment with columns :
The name of the signal.
A vector of the same size as copynumber containing the chromosome number.
The starting position of a segment.
The ending position of a segment.
The number of probes in the segment.
Means of the segment.
Quentin Grimonprez