This function sorts a dataset file by the genomic position of the probes.

This function sorts a dataset file by the genomic position of the probes. This function makes very easy the integration of VegaMC with the output of PennCNV tool.

Usage

sortData(dataset, output_file_name = "")

Arguments

dataset: Dataset file.
output_file_name: Name of the file in which sorted data are stored.

Value

This function returns the input matrix ordered by the genomic position of the probes.

References

Morganella S., and Ceccarelli M. VegaMC: a R/bioconductor package for fast downstream analysis of large array comparative genomic hybridization datasets. Bioinformatics, 28(19):2512-4 (2012).

Author

Sandro Morganella

Note

This function allows to sort a dataset by the genomic position. The input file must have the chromosome and the position in column two and three respectively. This format follows the standard output of PennCNV. An example of file can be found in inst/example folder.

Examples

if (FALSE) { # \dontrun{
    ## Copy the example dataset in current folder
    file.copy(system.file("example/breast_Affy500K.txt", package="VegaMC"), 
                            ".")


    ## Sort data and save results in sorted.txt file
    sortData("breast_Affy500K.txt", "sorted.txt")
} # }