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use Matrix library for sparse counts #294

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Sep 18, 2023
Merged

use Matrix library for sparse counts #294

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14848e8
use Matrix library for sparse counts
stemangiola Sep 8, 2023
6386415
Update DESCRIPTION
stemangiola Sep 14, 2023
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -35,7 +35,8 @@ Imports:
GenomicRanges,
methods,
S4Vectors,
crayon
crayon,
Matrix
Suggests:
BiocStyle,
testthat,
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1 change: 1 addition & 0 deletions NAMESPACE
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Expand Up @@ -83,6 +83,7 @@ import(preprocessCore)
import(readr)
import(tibble)
importFrom(GenomicRanges,makeGRangesListFromDataFrame)
importFrom(Matrix,colSums)
importFrom(S4Vectors,metadata)
importFrom(SummarizedExperiment,SummarizedExperiment)
importFrom(SummarizedExperiment,assays)
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3 changes: 2 additions & 1 deletion R/methods_SE.R
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Expand Up @@ -1584,6 +1584,7 @@ setMethod("keep_variable",
#'
#' @importFrom purrr map_chr
#' @importFrom tidyr unite
#' @importFrom Matrix colSums
#'
#' @docType methods
#' @rdname keep_variable-methods
Expand Down Expand Up @@ -1711,7 +1712,7 @@ setMethod("keep_variable",
min.count = minimum_counts,
group = string_factor_of_interest,
min.prop = minimum_proportion,
lib.size = colSums(., na.rm=TRUE)
lib.size = Matrix::colSums(., na.rm=TRUE)
) %>%
not() %>%
which %>%
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