load_markers: This function create the marker descriptor object containing...

In gaia: GAIA: An R package for genomic analysis of significant chromosomal aberrations.

Description

This function loads the markers contained within the matrix passed as argument and creates for all chromosomes an ordered vector containing the position of each marker.These vectors are loaded within a list.

Usage

load_markers(marker_matrix)

Arguments

marker_matrix

contains the marker descriptions as a matrix with the following structure: Probe Name - Chromosome - Start - End Note that the End position column is optional (in this case start and the end positions coincide). The sex chromosomes X and Y must be indicated with 23 and 24 respectively.

Value

This function returns a list having the following structure:

chromosome_marker_list[[i]]

is a matrix of dimension 2xN (N is the number of observed probes for the i-th chromosome) the first and the second row contains the start and the end position of each marker of the i-th chromosome respectively.

An example of the data produced by this function can be found in synthMarkers.

Author(s)

Sandro Morganella et al.

Maintainer: S. Morganella <[e-mail]>

Examples

# Load the matrix containing the informations about the markers
data(synthMarkers_Matrix)

# Use the function load_markers to obtain the marker descriptor data object
marks <- load_markers(synthMarkers_Matrix)

Example output

Loading Marker Informations
........................
Done

gaia documentation built on Nov. 8, 2020, 8:02 p.m.