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


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Documentation for package ‘gaia’ version 2.26.0

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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.