gedAlgorithm
provides access to the registered
gene expression deconvolution algorithms.
gedAlgorithmInfo
prints information about the
registered gene expression deconvolution or returns --
invisibly -- the complete algorithm registry, as a
registry
object.
gedAlgorithm(key, error = TRUE, exact = FALSE, all = FALSE, ...) gedAlgorithmInfo(show = TRUE, all = !show)
FALSE
then function
returns NULL
if the key is not found or NA
in case of multiple matches.key
is
missing and indicates if all registered keys should be
returned, including the internal one -- whose key starts
with a '.'.FALSE
) or only returned
invisibly (FALSE
).
gedAlgorithm()
## [1] "lsfit" "cs-lsfit" "qprog" "cs-qprog" "DSA"
## [6] "csSAM" "DSection" "ssKL" "ssFrobenius" "meanProfile"
## [11] "deconf"
gedAlgorithm('ssKL')
## <Object of class: GEDStrategy>
## Key: ssKL
## Require: Marker
## Reference: Gaujoux et al. (2011)
gedAlgorithm('csSAM')
## <Object of class: GEDStrategy>
## Key: csSAM
## Require: Coef
## Reference: Shen-Orr et al. (2010)
# show algorithms and properties
gedAlgorithmInfo()
## Description
## lsfit Partial deconvolution of proportions using least-squares fits
## cs-lsfit Partial deconvolution of cell signatures using least-squares fits
## qprog Estimates proportions from known expression signatures using quadratic programming
## cs-qprog Estimates constrained cell-specific signatures from proportions using quadratic programming [experimental]
## DSA Complete deconvolution using Digital Sorting Algorithm
## csSAM Estimates cell/tissue specific signatures from known proportions using SAM
## DSection Estimates proportions from proportions priors using MCMC
## ssKL Semi-supervised NMF algorithm for KL divergence, using marker genes
## ssFrobenius Semi-supervised NMF algorithm for Euclidean distance, using marker genes
## meanProfile Compute proportion proxies as mean expression profiles
## deconf Alternate least-square NMF method, using heuristic constraints
## Basis Coef Marker Iter Reference
## lsfit I O - 1 Abbas2009
## cs-lsfit O I - 1
## qprog I O - 1 Gong2011
## cs-qprog O I - 1
## DSA O O I 1 Zhong2013
## csSAM O I O 1 Shen-Orr2010
## DSection O I/O O 500 Erkkila2010
## ssKL O O I 3000 Gaujoux2011
## ssFrobenius O O I 3000 Gaujoux2011
## meanProfile - O I 1
## deconf O O - 1000 Repsilber2010
class(gedAlgorithmInfo(show=FALSE))
## [1] "GEDalgorithm_registry" "algorithms_package_registry"
## [3] "package_registry" "registry"