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

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This package allows to assess the statistical significance of chromosomal aberrations.

Author
Sandro Morganella et al.
Date of publication
None
Maintainer
S. Morganella <sandro@ebi.ac.uk>
License
GPL-2
Version
2.18.0

View on Bioconductor

Man pages

crc
Real aCGH Dataset of Colorectal Cancer (CRC)
crc_markers
Markers Descriptors for Real aCGH Dataset of Colorectal...
gaia-package
GAIA: An R package for genomic analysis of significant...
generate_approx_null_hypothesis
This function computes the probability distribution of the...
generate_null_hypothesis
This function computes the probability distribution of the...
load_cnv
This function create the object containing all needed...
load_markers
This function create the marker descriptor object containing...
peel_off
The iterative peel-off procedure to extract the independent...
qvalue
The procedure to compute the q-value.
runGAIA
Run GAIA algorithm.
search_peaks_in_regions
This function extracts the primary peak within a...
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...

Files in this package

gaia/DESCRIPTION
gaia/NAMESPACE
gaia/R
gaia/R/generate_approx_null_hypothesis.R
gaia/R/generate_null_hypothesis.R
gaia/R/load_cnv.R
gaia/R/load_markers.R
gaia/R/peel_off.R
gaia/R/qvalue.R
gaia/R/runGAIA.R
gaia/R/search_peaks_in_regions.R
gaia/R/write_significant_regions.R
gaia/build
gaia/build/vignette.rds
gaia/data
gaia/data/crc.RData
gaia/data/crc_markers.RData
gaia/data/synthCNV_Matrix.rda
gaia/data/synthMarkers_Matrix.rda
gaia/inst
gaia/inst/doc
gaia/inst/doc/gaia.R
gaia/inst/doc/gaia.Rnw
gaia/inst/doc/gaia.pdf
gaia/man
gaia/man/crc.Rd
gaia/man/crc_markers.Rd
gaia/man/gaia-package.Rd
gaia/man/generate_approx_null_hypothesis.Rd
gaia/man/generate_null_hypothesis.Rd
gaia/man/load_cnv.Rd
gaia/man/load_markers.Rd
gaia/man/peel_off.Rd
gaia/man/qvalue.Rd
gaia/man/runGAIA.Rd
gaia/man/search_peaks_in_regions.Rd
gaia/man/synthCNV_Matrix.Rd
gaia/man/synthMarkers_Matrix.Rd
gaia/man/write_significant_regions.Rd
gaia/vignettes
gaia/vignettes/gaia.Rnw