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

In VegaMC: VegaMC: A Package Implementing a Variational Piecewise Smooth Model for Identification of Driver Chromosomal Imbalances in Cancer

Description

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.

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.

Author(s)

Sandro Morganella

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).

Examples

    ## 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");

VegaMC documentation built on Nov. 8, 2020, 6:48 p.m.