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rescaleByNeighbors errors when input matrix is DelayedMatrix #5

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PeteHaitch opened this issue Mar 12, 2023 · 9 comments
Closed

rescaleByNeighbors errors when input matrix is DelayedMatrix #5

PeteHaitch opened this issue Mar 12, 2023 · 9 comments

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@PeteHaitch
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Should this work?

# Example adapted from ?rescaleByNeighbors
suppressPackageStartupMessages(library(mumosa))

suppressPackageStartupMessages(library(scater))
sce <- mockSCE()
sce <- logNormCounts(sce)
sce <- runPCA(sce)

adt_sce <- mockSCE(ngenes=20)
adt_sce <- logNormCounts(adt_sce)
altExp(sce, "ADT") <- adt_sce

# Works when ADT logcounts are matrix.
class(reducedDim(sce, "PCA"))
#> [1] "matrix" "array"
class(logcounts(altExp(sce, "ADT")))
#> [1] "matrix" "array"
combined <- rescaleByNeighbors(sce, dimreds="PCA", altexps="ADT")

# Errors when ADT logcounts are DelayedMatrix.
suppressPackageStartupMessages(library(DelayedArray))
logcounts(altExp(sce, "ADT")) <- DelayedArray(
  logcounts(altExp(sce, "ADT")))
class(reducedDim(sce, "PCA"))
#> [1] "matrix" "array"
class(logcounts(altExp(sce, "ADT")))
#> [1] "DelayedMatrix"
#> attr(,"package")
#> [1] "DelayedArray"
combined <- rescaleByNeighbors(sce, dimreds="PCA", altexps="ADT")
#> Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'bindCOLS' for signature '"matrix"'
Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.2 Patched (2022-11-10 r83330)
#>  os       Ubuntu 22.04.2 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en_AU:en
#>  collate  en_AU.UTF-8
#>  ctype    en_AU.UTF-8
#>  tz       Australia/Melbourne
#>  date     2023-03-13
#>  pandoc   2.19.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package              * version   date (UTC) lib source
#>  batchelor              1.14.1    2023-01-03 [1] Bioconductor
#>  beachmat               2.14.0    2022-11-01 [1] Bioconductor
#>  beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.2.2)
#>  Biobase              * 2.58.0    2022-11-01 [1] Bioconductor
#>  BiocGenerics         * 0.44.0    2022-11-01 [1] Bioconductor
#>  BiocNeighbors          1.16.0    2022-11-01 [1] Bioconductor
#>  BiocParallel           1.32.5    2022-12-23 [1] Bioconductor
#>  BiocSingular           1.14.0    2022-11-01 [1] Bioconductor
#>  bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.2.2)
#>  bluster                1.8.0     2022-11-01 [1] Bioconductor
#>  cli                    3.6.0     2023-01-09 [1] CRAN (R 4.2.2)
#>  cluster                2.1.4     2022-08-22 [1] CRAN (R 4.2.2)
#>  codetools              0.2-19    2023-02-01 [1] CRAN (R 4.2.2)
#>  colorspace             2.1-0     2023-01-23 [1] CRAN (R 4.2.2)
#>  DelayedArray         * 0.24.0    2022-11-01 [1] Bioconductor
#>  DelayedMatrixStats     1.20.0    2022-11-01 [1] Bioconductor
#>  digest                 0.6.31    2022-12-11 [1] CRAN (R 4.2.2)
#>  dplyr                  1.1.0     2023-01-29 [1] CRAN (R 4.2.2)
#>  dqrng                  0.3.0     2021-05-01 [1] CRAN (R 4.2.2)
#>  edgeR                  3.40.2    2023-01-19 [1] Bioconductor
#>  evaluate               0.20      2023-01-17 [1] CRAN (R 4.2.2)
#>  fansi                  1.0.4     2023-01-22 [1] CRAN (R 4.2.2)
#>  fastmap                1.1.1     2023-02-24 [1] CRAN (R 4.2.2)
#>  fs                     1.6.1     2023-02-06 [1] CRAN (R 4.2.2)
#>  generics               0.1.3     2022-07-05 [1] CRAN (R 4.2.2)
#>  GenomeInfoDb         * 1.34.9    2023-02-02 [1] Bioconductor
#>  GenomeInfoDbData       1.2.9     2022-11-04 [1] Bioconductor
#>  GenomicRanges        * 1.50.2    2022-12-16 [1] Bioconductor
#>  ggbeeswarm             0.7.1     2022-12-16 [1] CRAN (R 4.2.2)
#>  ggplot2              * 3.4.1     2023-02-10 [1] CRAN (R 4.2.2)
#>  ggrepel                0.9.3     2023-02-03 [1] CRAN (R 4.2.2)
#>  glue                   1.6.2     2022-02-24 [1] CRAN (R 4.2.2)
#>  gridExtra              2.3       2017-09-09 [1] CRAN (R 4.2.2)
#>  gtable                 0.3.1     2022-09-01 [1] CRAN (R 4.2.2)
#>  htmltools              0.5.4     2022-12-07 [1] CRAN (R 4.2.2)
#>  igraph                 1.4.1     2023-02-24 [1] CRAN (R 4.2.2)
#>  IRanges              * 2.32.0    2022-11-01 [1] Bioconductor
#>  irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.2.2)
#>  knitr                  1.42      2023-01-25 [1] CRAN (R 4.2.2)
#>  lattice                0.20-45   2021-09-22 [1] CRAN (R 4.2.2)
#>  lifecycle              1.0.3     2022-10-07 [1] CRAN (R 4.2.2)
#>  limma                  3.54.2    2023-02-28 [1] Bioconductor
#>  locfit                 1.5-9.7   2023-01-02 [1] CRAN (R 4.2.2)
#>  magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.2.2)
#>  Matrix               * 1.5-3     2022-11-11 [1] CRAN (R 4.2.2)
#>  MatrixGenerics       * 1.10.0    2022-11-01 [1] Bioconductor
#>  matrixStats          * 0.63.0    2022-11-18 [1] CRAN (R 4.2.2)
#>  metapod                1.6.0     2022-11-01 [1] Bioconductor
#>  mumosa               * 1.6.0     2022-11-01 [1] Bioconductor
#>  munsell                0.5.0     2018-06-12 [1] CRAN (R 4.2.2)
#>  pillar                 1.8.1     2022-08-19 [1] CRAN (R 4.2.2)
#>  pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.2.2)
#>  purrr                  1.0.1     2023-01-10 [1] CRAN (R 4.2.2)
#>  R6                     2.5.1     2021-08-19 [1] CRAN (R 4.2.2)
#>  Rcpp                   1.0.10    2023-01-22 [1] CRAN (R 4.2.2)
#>  RCurl                  1.98-1.10 2023-01-27 [1] CRAN (R 4.2.2)
#>  reprex                 2.0.2     2022-08-17 [1] CRAN (R 4.2.2)
#>  ResidualMatrix         1.8.0     2022-11-01 [1] Bioconductor
#>  rlang                  1.0.6     2022-09-24 [1] CRAN (R 4.2.2)
#>  rmarkdown              2.20      2023-01-19 [1] CRAN (R 4.2.2)
#>  rstudioapi             0.14      2022-08-22 [1] CRAN (R 4.2.2)
#>  rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.2.2)
#>  S4Vectors            * 0.36.2    2023-02-26 [1] Bioconductor
#>  ScaledMatrix           1.6.0     2022-11-01 [1] Bioconductor
#>  scales                 1.2.1     2022-08-20 [1] CRAN (R 4.2.2)
#>  scater               * 1.26.1    2022-11-13 [1] Bioconductor
#>  scran                  1.26.2    2023-01-19 [1] Bioconductor
#>  scuttle              * 1.8.4     2023-01-19 [1] Bioconductor
#>  sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.2.2)
#>  SingleCellExperiment * 1.20.0    2022-11-01 [1] Bioconductor
#>  sparseMatrixStats      1.10.0    2022-11-01 [1] Bioconductor
#>  statmod                1.5.0     2023-01-06 [1] CRAN (R 4.2.2)
#>  SummarizedExperiment * 1.28.0    2022-11-01 [1] Bioconductor
#>  tibble                 3.2.0     2023-03-08 [1] CRAN (R 4.2.2)
#>  tidyselect             1.2.0     2022-10-10 [1] CRAN (R 4.2.2)
#>  utf8                   1.2.3     2023-01-31 [1] CRAN (R 4.2.2)
#>  uwot                   0.1.14    2022-08-22 [1] CRAN (R 4.2.2)
#>  vctrs                  0.5.2     2023-01-23 [1] CRAN (R 4.2.2)
#>  vipor                  0.4.5     2017-03-22 [1] CRAN (R 4.2.2)
#>  viridis                0.6.2     2021-10-13 [1] CRAN (R 4.2.2)
#>  viridisLite            0.4.1     2022-08-22 [1] CRAN (R 4.2.2)
#>  withr                  2.5.0     2022-03-03 [1] CRAN (R 4.2.2)
#>  xfun                   0.37      2023-01-31 [1] CRAN (R 4.2.2)
#>  XVector                0.38.0    2022-11-01 [1] Bioconductor
#>  yaml                   2.3.7     2023-01-23 [1] CRAN (R 4.2.2)
#>  zlibbioc               1.44.0    2022-11-01 [1] Bioconductor
#> 
#>  [1] /home/peter/R/x86_64-pc-linux-gnu-library/4.2
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────
@PeteHaitch
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FWIW in my case, I ended up with a DelayedMatrix as the ADT logcounts after using combineCols() (similar to the below).
Is this a bug in combineCols() not respecting delayed = FALSE for the altExps?
I'll post a new issue if so.

suppressPackageStartupMessages(library(scater))
sce <- mockSCE()
sce <- logNormCounts(sce)
sce <- runPCA(sce)

adt_sce <- mockSCE(ngenes=20)
adt_sce <- logNormCounts(adt_sce)
altExp(sce, "ADT") <- adt_sce

sce2 <- combineCols(sce, sce, delayed = FALSE, fill = 0)
class(logcounts(sce2))
#> [1] "matrix" "array"
class(logcounts(altExp(sce2, "ADT")))
#> [1] "DelayedMatrix"
#> attr(,"package")
#> [1] "DelayedArray"
Session info 
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#>  setting  value
#>  version  R version 4.2.2 Patched (2022-11-10 r83330)
#>  os       Ubuntu 22.04.2 LTS
#>  system   x86_64, linux-gnu
#>  ui       X11
#>  language en_AU:en
#>  collate  en_AU.UTF-8
#>  ctype    en_AU.UTF-8
#>  tz       Australia/Melbourne
#>  date     2023-03-13
#>  pandoc   2.19.2 @ /usr/lib/rstudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#> 
#> ─ Packages ───────────────────────────────────────────────────────────────────
#>  package              * version   date (UTC) lib source
#>  beachmat               2.14.0    2022-11-01 [1] Bioconductor
#>  beeswarm               0.4.0     2021-06-01 [1] CRAN (R 4.2.2)
#>  Biobase              * 2.58.0    2022-11-01 [1] Bioconductor
#>  BiocGenerics         * 0.44.0    2022-11-01 [1] Bioconductor
#>  BiocNeighbors          1.16.0    2022-11-01 [1] Bioconductor
#>  BiocParallel           1.32.5    2022-12-23 [1] Bioconductor
#>  BiocSingular           1.14.0    2022-11-01 [1] Bioconductor
#>  bitops                 1.0-7     2021-04-24 [1] CRAN (R 4.2.2)
#>  cli                    3.6.0     2023-01-09 [1] CRAN (R 4.2.2)
#>  codetools              0.2-19    2023-02-01 [1] CRAN (R 4.2.2)
#>  colorspace             2.1-0     2023-01-23 [1] CRAN (R 4.2.2)
#>  DelayedArray           0.24.0    2022-11-01 [1] Bioconductor
#>  DelayedMatrixStats     1.20.0    2022-11-01 [1] Bioconductor
#>  digest                 0.6.31    2022-12-11 [1] CRAN (R 4.2.2)
#>  dplyr                  1.1.0     2023-01-29 [1] CRAN (R 4.2.2)
#>  evaluate               0.20      2023-01-17 [1] CRAN (R 4.2.2)
#>  fansi                  1.0.4     2023-01-22 [1] CRAN (R 4.2.2)
#>  fastmap                1.1.1     2023-02-24 [1] CRAN (R 4.2.2)
#>  fs                     1.6.1     2023-02-06 [1] CRAN (R 4.2.2)
#>  generics               0.1.3     2022-07-05 [1] CRAN (R 4.2.2)
#>  GenomeInfoDb         * 1.34.9    2023-02-02 [1] Bioconductor
#>  GenomeInfoDbData       1.2.9     2022-11-04 [1] Bioconductor
#>  GenomicRanges        * 1.50.2    2022-12-16 [1] Bioconductor
#>  ggbeeswarm             0.7.1     2022-12-16 [1] CRAN (R 4.2.2)
#>  ggplot2              * 3.4.1     2023-02-10 [1] CRAN (R 4.2.2)
#>  ggrepel                0.9.3     2023-02-03 [1] CRAN (R 4.2.2)
#>  glue                   1.6.2     2022-02-24 [1] CRAN (R 4.2.2)
#>  gridExtra              2.3       2017-09-09 [1] CRAN (R 4.2.2)
#>  gtable                 0.3.1     2022-09-01 [1] CRAN (R 4.2.2)
#>  htmltools              0.5.4     2022-12-07 [1] CRAN (R 4.2.2)
#>  IRanges              * 2.32.0    2022-11-01 [1] Bioconductor
#>  irlba                  2.3.5.1   2022-10-03 [1] CRAN (R 4.2.2)
#>  knitr                  1.42      2023-01-25 [1] CRAN (R 4.2.2)
#>  lattice                0.20-45   2021-09-22 [1] CRAN (R 4.2.2)
#>  lifecycle              1.0.3     2022-10-07 [1] CRAN (R 4.2.2)
#>  magrittr               2.0.3     2022-03-30 [1] CRAN (R 4.2.2)
#>  Matrix                 1.5-3     2022-11-11 [1] CRAN (R 4.2.2)
#>  MatrixGenerics       * 1.10.0    2022-11-01 [1] Bioconductor
#>  matrixStats          * 0.63.0    2022-11-18 [1] CRAN (R 4.2.2)
#>  munsell                0.5.0     2018-06-12 [1] CRAN (R 4.2.2)
#>  pillar                 1.8.1     2022-08-19 [1] CRAN (R 4.2.2)
#>  pkgconfig              2.0.3     2019-09-22 [1] CRAN (R 4.2.2)
#>  purrr                  1.0.1     2023-01-10 [1] CRAN (R 4.2.2)
#>  R6                     2.5.1     2021-08-19 [1] CRAN (R 4.2.2)
#>  Rcpp                   1.0.10    2023-01-22 [1] CRAN (R 4.2.2)
#>  RCurl                  1.98-1.10 2023-01-27 [1] CRAN (R 4.2.2)
#>  reprex                 2.0.2     2022-08-17 [1] CRAN (R 4.2.2)
#>  rlang                  1.0.6     2022-09-24 [1] CRAN (R 4.2.2)
#>  rmarkdown              2.20      2023-01-19 [1] CRAN (R 4.2.2)
#>  rstudioapi             0.14      2022-08-22 [1] CRAN (R 4.2.2)
#>  rsvd                   1.0.5     2021-04-16 [1] CRAN (R 4.2.2)
#>  S4Vectors            * 0.36.2    2023-02-26 [1] Bioconductor
#>  ScaledMatrix           1.6.0     2022-11-01 [1] Bioconductor
#>  scales                 1.2.1     2022-08-20 [1] CRAN (R 4.2.2)
#>  scater               * 1.26.1    2022-11-13 [1] Bioconductor
#>  scuttle              * 1.8.4     2023-01-19 [1] Bioconductor
#>  sessioninfo            1.2.2     2021-12-06 [1] CRAN (R 4.2.2)
#>  SingleCellExperiment * 1.20.0    2022-11-01 [1] Bioconductor
#>  sparseMatrixStats      1.10.0    2022-11-01 [1] Bioconductor
#>  SummarizedExperiment * 1.28.0    2022-11-01 [1] Bioconductor
#>  tibble                 3.2.0     2023-03-08 [1] CRAN (R 4.2.2)
#>  tidyselect             1.2.0     2022-10-10 [1] CRAN (R 4.2.2)
#>  utf8                   1.2.3     2023-01-31 [1] CRAN (R 4.2.2)
#>  vctrs                  0.5.2     2023-01-23 [1] CRAN (R 4.2.2)
#>  vipor                  0.4.5     2017-03-22 [1] CRAN (R 4.2.2)
#>  viridis                0.6.2     2021-10-13 [1] CRAN (R 4.2.2)
#>  viridisLite            0.4.1     2022-08-22 [1] CRAN (R 4.2.2)
#>  withr                  2.5.0     2022-03-03 [1] CRAN (R 4.2.2)
#>  xfun                   0.37      2023-01-31 [1] CRAN (R 4.2.2)
#>  XVector                0.38.0    2022-11-01 [1] Bioconductor
#>  yaml                   2.3.7     2023-01-23 [1] CRAN (R 4.2.2)
#>  zlibbioc               1.44.0    2022-11-01 [1] Bioconductor
#> 
#>  [1] /home/peter/R/x86_64-pc-linux-gnu-library/4.2
#>  [2] /usr/local/lib/R/site-library
#>  [3] /usr/lib/R/site-library
#>  [4] /usr/lib/R/library
#> 
#> ──────────────────────────────────────────────────────────────────────────────

@LTLA
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LTLA commented Mar 13, 2023 

#> Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'bindCOLS' for signature '"matrix"'

I'm... not sure. I don't even see a bindCOLS in my code. What does the traceback() say?

class(logcounts(altExp(sce2, "ADT")))
#> [1] "DelayedMatrix"
#> attr(,"package")
#> [1] "DelayedArray"

Probably forgot to forward delayed=FALSE to the combineCols call on the alternative experiments in the SCE method.

https://github.com/drisso/SingleCellExperiment/blob/07eb78ae4dae9dbc44f64dc3796fdfd55353aa4e/R/combine.R#L311

Could post an issue there. Or make a PR.

@PeteHaitch
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I'm... not sure. I don't even see a bindCOLS in my code. What does the traceback() say?

> traceback()
20: stop(gettextf("unable to find an inherited method for function %s for signature %s", 
        sQuote(fdef@generic), sQuote(cnames)), domain = NA)
19: (function (classes, fdef, mtable) 
    {
        methods <- .findInheritedMethods(classes, fdef, mtable)
        if (length(methods) == 1L) 
            return(methods[[1L]])
        else if (length(methods) == 0L) {
            cnames <- paste0("\"", vapply(classes, as.character, 
                ""), "\"", collapse = ", ")
            stop(gettextf("unable to find an inherited method for function %s for signature %s", 
                sQuote(fdef@generic), sQuote(cnames)), domain = NA)
        }
        else stop("Internal error in finding inherited methods; didn't return a unique method", 
            domain = NA)
    })(list("matrix"), new("standardGeneric", .Data = function (x, 
        objects = list(), use.names = TRUE, ignore.mcols = FALSE, 
        check = TRUE) 
    standardGeneric("bindCOLS"), generic = structure("bindCOLS", package = "S4Vectors"), 
        package = "S4Vectors", group = list(), valueClass = character(0), 
        signature = "x", default = NULL, skeleton = (function (x, 
            objects = list(), use.names = TRUE, ignore.mcols = FALSE, 
     ...
18: bindCOLS(objects[[1L]], objects = objects[-1L])
17: cbind(deparse.level, ...)
16: cbind(...)
15: eval(mc, env)
14: eval(mc, env)
13: eval(mc, env)
12: standardGeneric("cbind")
11: (new("standardGeneric", .Data = function (..., deparse.level = 1) 
    standardGeneric("cbind"), generic = structure("cbind", package = "BiocGenerics"), 
        package = "BiocGenerics", group = list(), valueClass = character(0), 
        signature = "...", default = new("derivedDefaultMethod", 
            .Data = function (..., deparse.level = 1) 
            .Internal(cbind(deparse.level, ...)), target = new("signature", 
                .Data = "ANY", names = "...", package = "methods"), 
            defined = new("signature", .Data = "ANY", names = "...", 
                package = "methods"), generic = structure("cbind", package = "base")), 
        skeleton = (new("derivedDefaultMethod", .Data = function (..., 
            deparse.level = 1) 
        .Internal(cbind(deparse.level, ...)), target = new("signature", 
            .Data = "ANY", names = "...", package = "methods"), defined = new("signature", 
            .Data = "ANY", names = "...", package = "methods"), generic = structure("cbind", package = "base")))(..., 
            deparse.level = deparse.level)))(structure(c(-0.189998917271939, 
    -0.0868457985158096, -0.0175665386822309, 0.051007506575224, 
    -0.079684254813382, 0.231026123993908, -0.0513426734347379, 0.00486179440517301, 
    0.0296294770372357, 0.146588831282046, 0.154727337375575, 0.149423773225478, 
    0.0125237799710574, -0.337186010692366, 0.202961678245827, 0.157990351312671, 
    0.0844648312825455, 0.102287825158096, -0.0648798900378344, 0.190372783013001, 
     ...
10: do.call(cbind, x)
9: .rescale_modal_matrices(c(targets, extras), ...)
8: .local(x, ...)
7: .nextMethod(x, assays = assays, extras = c(targets, extras), 
       ...)
6: eval(call, callEnv)
5: eval(call, callEnv)
4: callNextMethod(x, assays = assays, extras = c(targets, extras), 
       ...)
3: .local(x, ...)
2: rescaleByNeighbors(sce, dimreds = "PCA", altexps = "ADT")
1: rescaleByNeighbors(sce, dimreds = "PCA", altexps = "ADT")

Root cause to be a DelayedArray issue:

dim(reducedDim(sce, "PCA"))
#>  200  50
dim(t(logcounts(altExp(sce, "ADT"))))
#>  200  20
cbind(reducedDim(sce, "PCA"), t(logcounts(altExp(sce, "ADT"))))
#> Error in (function (classes, fdef, mtable)  :  unable to find an inherited method for function ‘bindCOLS’ for signature ‘"matrix"’

@PeteHaitch
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Probably forgot to forward delayed=FALSE to the combineCols call on the alternative experiments in the SCE method.
https://github.com/drisso/SingleCellExperiment/blob/07eb78ae4dae9dbc44f64dc3796fdfd55353aa4e/R/combine.R#L311
Could post an issue there. Or make a PR.

In my quick look earlier I didn't see where delayed was supposed to be passed onto, but I'll take a look tomorrow.

@LTLA
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LTLA commented Mar 14, 2023

Possibly related: Bioconductor/DelayedArray#100

@LTLA
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LTLA commented Mar 14, 2023

Anyway, just pushed a workaround to master and BioC-devel - see if it works.

@PeteHaitch
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Will do.
PR incoming for combineCols() issue (#5 (comment))

PeteHaitch pushed a commit to PeteHaitch/SingleCellExperiment that referenced this issue Mar 14, 2023
Pass delayed and fill to combineCols() of altExps
f7158cc 
- Identified in LTLA/mumosa#5 (comment)
@PeteHaitch PeteHaitch mentioned this issue Mar 14, 2023
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@PeteHaitch
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PeteHaitch commented Mar 14, 2023 •
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Can confirm that 6d61b52 is a workaround for the headline issue.
Is the rationale that if any of the inputs are DelayedArray's then the output needs to be as well to avoid possibly blowing up memory?

@LTLA
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LTLA commented Mar 14, 2023

Yes, that's correct. In this case, I suspect it doesn't matter, because BiocNeighbors will probably coerce things to a matrix internally anyway, but that's a different issue.

LTLA pushed a commit to drisso/SingleCellExperiment that referenced this issue Mar 15, 2023
@PeteHaitch
Pass delayed and fill to combineCols() of altExps (#68)
6bb77c3 
This ensures that the treatment of the alternative experiment's assays
is consistent with that of the main experiment.

Identified in LTLA/mumosa#5 (comment)
LTLA pushed a commit to drisso/SingleCellExperiment that referenced this issue Mar 15, 2023
@PeteHaitch @LTLA
Pass delayed and fill to combineCols() of altExps (#68)
45f87e8 
This ensures that the treatment of the alternative experiment's assays
is consistent with that of the main experiment.

Identified in LTLA/mumosa#5 (comment)
@ycl6 ycl6 mentioned this issue Sep 25, 2024
Merged
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@PeteHaitch @LTLA