Description Usage Arguments Details Value Author(s) Examples
View source: R/getSymFracBsignal.R
Extract symmetrized allele B fraction signals from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.
1 2 3 4 5 6 7 | getSymFracBSignal(
dataSetName,
file,
chromosome,
normalTumorArray,
verbose = TRUE
)
|
dataSetName |
The name of the data-set folder (it must correpond to a folder name in rawData folder.) |
file |
The name of the file in dataSetName to extract. |
chromosome |
A vector with the chromosomes for which the symetrized signal will be extracted. |
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. |
verbose |
If TRUE, print some informations. |
The aroma architecture must be respected. The working directory must contain rawData folder and totalAndFracBData folder. To easily access the names of the files available in a dataset, one can use the getListOfFiles function.
a list of length the number of chromosome containing a data.frame with columns:
chromosome corresponding to the signal.
Positions associated to the allele B fraction.
One column named by the data file name. It contains the symmetrized allele B fraction signal for the specified profile.
Names of the probes.
Quentin Grimonprez
1 2 3 4 5 6 | ## Not run:
#DO NOT EXECUTE before reading the vignette
fracB=getSymFracBSignal("data1",5,normalTumorArray)
fracB=getSymFracBSignal("data2",5)
## End(Not run)
|
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