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

Documentation for package ‘gaia’ version 1.10.2

crc	Real aCGH Dataset of Colorectal Cancer (CRC)
crc_markers	Markers Descriptors for Real aCGH Dataset of Colorectal Cancer (CRC)
gaia	GAIA: An R package for genomic analysis of significant chromosomal aberrations.
generate_approx_null_hypothesis	This function computes the probability distribution of the null hypothesis by an approximation.
generate_null_hypothesis	This function computes the probability distribution of the null hypothesis.
load_cnv	This function create the object containing all needed informations about the aberrant regions.
load_markers	This function create the marker descriptor object containing all needed marker informations.
peel_off	The iterative peel-off procedure to extract the independent peak regions.
qvalue	The procedure to compute the q-value.
runGAIA	Run GAIA algorithm.
search_peaks_in_regions	This function extracts the primary peak within a well-specified region.
synthCNV_Matrix	Example of aberration descriptor data matrix
synthMarkers_Matrix	Example of marker descriptor data matrix
write_significant_regions	This function writes into a tab delimited file the significant aberrant regions.