Description Usage Arguments Details Value Author(s) Examples
View source: R/getGenotypeCalls.R
Extract genotype calls from aroma files. It requires to have executed the normalization process suggested by aroma packages, by using signalPreProcess for example.
1 | getGenotypeCalls(dataSetName, chromosome, listOfFiles = NULL, verbose = TRUE)
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dataSetName |
The name of the data-set folder (it must correspond to a folder name in rawData folder.) |
chromosome |
A vector containing the chromosomes for which the genotype call will be extracted. |
listOfFiles |
A vector containing the names of the files in dataSetName folder for which the genotype signal will be extracted (default is all the files). |
verbose |
If TRUE print some information (default=TRUE) |
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 chromosomes containing a data.frame with columns:
Chromosome of the signal.
Positions associated with the genotype.
Genotype calls corresponding to selected files; the name of each column is the name of the associated data file name.
Names of the probes.
Quentin Grimonprez
1 2 3 4 5 | ## Not run:
#DO NOT EXECUTE before reading the vignette
fracB=getGenotypeCalls("data1",5)
## End(Not run)
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