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Co-authored-by: Tuomas Borman <tvborm@utu.fi>
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antagomir
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Feb 20, 2026
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Seems good to me as is.
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| jointRPCAuniversal <- function(x, experiments = NULL, | ||
| transform = c("rclr", "none"), | ||
| optspace.tol = 1e-5, | ||
| center = TRUE, | ||
| scale = FALSE, | ||
| ...) { | ||
| transform <- match.arg(transform) | ||
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| assay_names_used <- NULL | ||
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| if (inherits(x, "MultiAssayExperiment")) { | ||
| mae <- .extract_mae_tables(x, experiments) | ||
| tables <- mae$tables | ||
| experiments <- mae$experiments | ||
| assay_names_used <- mae$assay_names_used | ||
| } else if (inherits(x, "SummarizedExperiment")) { | ||
| tables <- list(assay(x)) | ||
| anm <- assayNames(x) | ||
| nm <- if (length(anm) && !is.na(anm[1])) anm[1] else "assay1" | ||
| names(tables) <- nm | ||
| } else if (is.list(x) && all(vapply(x, is.matrix, logical(1)))) { | ||
| tables <- x | ||
| if (is.null(names(tables))) { | ||
| names(tables) <- paste0("view", seq_along(tables)) |
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It still lacks usage of generic functions, for instance.
Have @raivo-otus had time to check this? I could also dedicate time to this this week so that we get this done.
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We should proceed towards merging joint-rpca to devel.
Ideally we should get this included in the next Bioc release, there is still time.