Add SE and MAE support #351
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TuomasBorman
commented
Feb 12, 2025
| @@ -39,17 +41,16 @@ Authors@R: | |||
| person("Florian", "Rohart", role = "aut"), | |||
| person("Ignacio", "Gonzalez", role = "aut"), | |||
| person("Sebastien", "Dejean", role = "aut"), | |||
| ## key contributors | |||
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TuomasBorman
commented
Feb 12, 2025
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| setMethod("mixOmics", signature = c(X = "matrix"), function( | ||
| X, | ||
| Y, | ||
| indY, | ||
| study, | ||
| ncomp, | ||
| keepX, | ||
| keepY, | ||
| design, | ||
| tau = NULL, | ||
| mode = c("regression", "canonical", "invariant", "classic"), | ||
| scale, | ||
| tol = 1e-06, | ||
| max.iter = 100, | ||
| near.zero.var = FALSE){ | ||
| res <- internal_mixOmics( | ||
| X, | ||
| Y, | ||
| indY, | ||
| study, | ||
| ncomp, | ||
| keepX, | ||
| keepY, | ||
| design, | ||
| tau = NULL, | ||
| mode = c("regression", "canonical", "invariant", "classic"), | ||
| scale, | ||
| tol = 1e-06, | ||
| max.iter = 100, | ||
| near.zero.var = FALSE | ||
| ) | ||
| return(res) | ||
| } | ||
| ) | ||
|
|
||
| #' @rdname mixOmics | ||
| #' @export | ||
| setMethod("mixOmics", signature = c(X = "list"), function( | ||
| X, | ||
| Y, | ||
| indY, | ||
| study, | ||
| ncomp, | ||
| keepX, | ||
| keepY, | ||
| design, | ||
| tau = NULL, | ||
| mode = c("regression", "canonical", "invariant", "classic"), | ||
| scale, | ||
| tol = 1e-06, | ||
| max.iter = 100, | ||
| near.zero.var = FALSE, | ||
| ...){ | ||
| res <- internal_mixOmics( | ||
| X, | ||
| Y, | ||
| indY, | ||
| study, | ||
| ncomp, | ||
| keepX, | ||
| keepY, | ||
| design, | ||
| tau = NULL, | ||
| mode = c("regression", "canonical", "invariant", "classic"), | ||
| scale, | ||
| tol = 1e-06, | ||
| max.iter = 100, | ||
| near.zero.var = FALSE, | ||
| ... | ||
| ) | ||
| return(res) | ||
| } | ||
| ) | ||
|
|
||
| internal_mixOmics <- function(X, |
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The old mixOmics function is converted into generic function. Otherwise I have not touched the existing code
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Related to this issue: #347
This PR adds support for
SummarizedExperimentandMultiAssayExperimentclasses. They are primary data containers in Bioconductor which is why I think that the support benefits both mixOmics and whole Bioconductor ecosystem.