peel_off: The iterative peel-off procedure to extract the independent...
In gaia: GAIA: An R package for genomic analysis of significant chromosomal aberrations.
Description
This function implements the peel-off algorithm to extract the independent regions having the minimum q-value (lower than the given threshold) within each chromosome. The function returns for each aberration and for each chromosome the list of aberrant regions. This function uses as support the function search_peaks_in_region that extract the primary peaks.
Note
This function uses the R package qvalue available at the bioconductor repository.
To install the qvalue package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("qvalue")
Author(s)
Sandro Morganella et al.
Maintainer: S. Morganella <morganellaalx@gmail.com>
gaia documentation built on Nov. 8, 2020, 8:02 p.m.
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Description
This function implements the peel-off algorithm to extract the independent regions having the minimum q-value (lower than the given threshold) within each chromosome. The function returns for each aberration and for each chromosome the list of aberrant regions. This function uses as support the function search_peaks_in_region that extract the primary peaks.
Note
This function uses the R package qvalue available at the bioconductor repository.
To install the qvalue package, start R and enter:
if (!requireNamespace("BiocManager", quietly=TRUE))
install.packages("BiocManager")
BiocManager::install("qvalue")
Author(s)
Sandro Morganella et al.
Maintainer: S. Morganella <morganellaalx@gmail.com>
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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