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

## Documentation for package ‘gaia’ version 2.16.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.