Hi,
I have tried using satuRn in a dataset for differential isoform usage on the transcript level. I really like the package, and previously it worked on another dataset for me. However, for this dataset (which is very similar to the previous one) I get an error when the algorithm is computing local FDR. I get the error:
Error in if (bett[2] > 0) bett = bet + 0.1 * solve(V, Y - mu)/(1 + 1/j^2) :
missing value where TRUE/FALSE needed
The way I understand it is that during the first time locfdr_locmle() is called, it fills the mlests with NA values, since my bett[2] is 0.77 (so if (bett[2] >= 0) {mle = rep(NA, 6)). Then the second time locfdr_locmle() is called, it tries to use the values from mlests, but these have been set to NA. Can you help me with this issue? I am not sure if this is something that I am supposed to "fix" or not, but this error feels more technical to me rather than that the input data is bad, but I do not understand the statistics behind it. I hope you can help me and I am curious if you have any insights in this.
Best wishes,
Tijs
#### start code from locFDR package
N <- length(zvalues_mid)
b <- 4.3 * exp(-0.26 * log(N, 10))
med <- median(zvalues_mid)
sc <- diff(quantile(zvalues_mid)[c(2, 4)]) / (2 * qnorm(.75))
# initial MLEs of empirical null parameters
mlests <- locfdr_locmle(zvalues_mid, xlim = c(med, b * sc))
lo <- min(zvalues_mid)
up <- max(zvalues_mid)
bre <- 120
breaks <- seq(lo, up, length = bre)
zzz <- pmax(pmin(zvalues_mid, up), lo)
zh <- hist(zzz, breaks = breaks, plot = FALSE)
x <- (breaks[-1] + breaks[-length(breaks)]) / 2
sw <- 0
X <- cbind(1, poly(x, df = 7))
zh <- hist(zzz, breaks = breaks, plot = FALSE)
y <- zh$counts
f <- glm(y ~ poly(x, df = 7), poisson)$fit
Cov.in <- list(x = x, X = X, f = f, sw = sw)
ml.out <- locfdr_locmle(zvalues_mid,
xlim = c(mlests[1], b * mlests[2]),
d = mlests[1], s = mlests[2], Cov.in = Cov.in
) # updated MLEs of empirical null parameters
mlests <- ml.out$mle
#### end code from locFDR package
R session information
sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.3 (2025-02-28)
os AlmaLinux 9.5 (Teal Serval)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Brussels
date 2025-04-14
rstudio 2024.12.0+467 Kousa Dogwood (server)
pandoc 3.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
quarto 1.5.57 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.4.1)
annotate 1.82.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
AnnotationDbi * 1.66.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
Biobase * 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocFileCache 2.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocGenerics * 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocManager 1.30.25 2024-08-28 [1] CRAN (R 4.4.1)
BiocParallel * 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
biomaRt 2.60.1 2024-06-26 [1] Bioconductor 3.19 (R 4.4.1)
Biostrings 2.72.1 2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
bit 4.6.0 2025-03-06 [1] CRAN (R 4.4.3)
bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.4.3)
bitops 1.0-9 2024-10-03 [1] CRAN (R 4.4.1)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
boot 1.3-31 2024-08-28 [2] CRAN (R 4.4.3)
bslib 0.9.0 2025-01-30 [1] CRAN (R 4.4.3)
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
cli 3.6.4 2025-02-13 [1] CRAN (R 4.4.3)
codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.3)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.4.1)
conflicted * 1.2.0 2023-02-01 [1] CRAN (R 4.4.0)
crayon 1.5.3 2024-06-20 [1] CRAN (R 4.4.0)
curl 6.2.2 2025-03-24 [1] CRAN (R 4.4.3)
data.table * 1.17.0 2025-02-22 [1] CRAN (R 4.4.3)
DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0)
DelayedArray 0.30.1 2024-05-07 [1] Bioconductor 3.19 (R 4.4.0)
DESeq2 * 1.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
DEXSeq * 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
dplyr * 1.1.4 2023-11-17 [1] CRAN (R 4.4.0)
evaluate 1.0.3 2025-01-10 [1] CRAN (R 4.4.3)
fastmap 1.2.0 2024-05-15 [1] CRAN (R 4.4.0)
filelock 1.0.3 2023-12-11 [1] CRAN (R 4.4.0)
forcats * 1.0.0 2023-01-29 [1] CRAN (R 4.4.0)
genefilter 1.86.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
geneplotter 1.82.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
generics 0.1.3 2022-07-05 [1] CRAN (R 4.4.0)
GenomeInfoDb * 1.40.1 2024-05-24 [1] Bioconductor 3.19 (R 4.4.0)
GenomeInfoDbData 1.2.12 2024-05-22 [1] Bioconductor
GenomicRanges * 1.56.2 2024-10-09 [1] Bioconductor 3.19 (R 4.4.1)
ggplot2 * 3.5.2 2025-04-09 [1] CRAN (R 4.4.3)
glue 1.8.0 2024-09-30 [1] CRAN (R 4.4.1)
gtable 0.3.6 2024-10-25 [1] CRAN (R 4.4.1)
hms 1.1.3 2023-03-21 [1] CRAN (R 4.4.0)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.4.0)
httr 1.4.7 2023-08-15 [1] CRAN (R 4.4.0)
httr2 1.1.2 2025-03-26 [1] CRAN (R 4.4.3)
hwriter 1.3.2.1 2022-04-08 [1] CRAN (R 4.4.0)
IRanges * 2.38.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.4.0)
jsonlite 2.0.0 2025-03-27 [1] CRAN (R 4.4.3)
KEGGREST 1.44.1 2024-06-19 [1] Bioconductor 3.19 (R 4.4.0)
knitr 1.50 2025-03-16 [1] CRAN (R 4.4.3)
lattice 0.22-6 2024-03-20 [2] CRAN (R 4.4.3)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.4.0)
limma 3.60.6 2024-10-02 [1] Bioconductor 3.19 (R 4.4.1)
locfdr 1.1-8 2015-07-15 [1] CRAN (R 4.4.3)
locfit 1.5-9.12 2025-03-05 [1] CRAN (R 4.4.3)
lubridate * 1.9.4 2024-12-08 [1] CRAN (R 4.4.3)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.4.0)
Matrix 1.7-2 2025-01-23 [2] CRAN (R 4.4.3)
MatrixGenerics * 1.16.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
matrixStats * 1.5.0 2025-01-07 [1] CRAN (R 4.4.3)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.4.0)
munsell 0.5.1 2024-04-01 [1] CRAN (R 4.4.0)
pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.4.0)
pillar 1.10.2 2025-04-05 [1] CRAN (R 4.4.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
prettyunits 1.2.0 2023-09-24 [1] CRAN (R 4.4.0)
progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.1)
purrr * 1.0.4 2025-02-05 [1] CRAN (R 4.4.3)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.4.3)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.0)
RColorBrewer * 1.1-3 2022-04-03 [1] CRAN (R 4.4.0)
Rcpp 1.0.14 2025-01-12 [1] CRAN (R 4.4.3)
readr * 2.1.5 2024-01-10 [1] CRAN (R 4.4.0)
rlang 1.1.5 2025-01-17 [1] CRAN (R 4.4.3)
rmarkdown 2.29 2024-11-04 [1] CRAN (R 4.4.1)
Rsamtools 2.20.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
RSQLite 2.3.9 2024-12-03 [1] CRAN (R 4.4.2)
rstudioapi 0.17.1 2024-10-22 [1] CRAN (R 4.4.1)
S4Arrays 1.4.1 2024-05-20 [1] Bioconductor 3.19 (R 4.4.0)
S4Vectors * 0.42.1 2024-07-03 [1] Bioconductor 3.19 (R 4.4.1)
sass 0.4.9 2024-03-15 [1] CRAN (R 4.4.0)
satuRn * 1.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.2)
scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
sessioninfo 1.2.3 2025-02-05 [1] CRAN (R 4.4.3)
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stageR 1.26.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
statmod 1.5.0 2023-01-06 [1] CRAN (R 4.4.0)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.4.3)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
SummarizedExperiment * 1.34.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
survival 3.8-3 2024-12-17 [1] CRAN (R 4.4.3)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0)
timechange 0.3.0 2024-01-18 [1] CRAN (R 4.4.0)
tzdb 0.5.0 2025-03-15 [1] CRAN (R 4.4.3)
UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
xfun 0.52 2025-04-02 [1] CRAN (R 4.4.3)
XML 3.99-0.18 2025-01-01 [1] CRAN (R 4.4.3)
xml2 1.3.8 2025-03-14 [1] CRAN (R 4.4.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.4.0)
XVector 0.44.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
yaml 2.3.10 2024-07-26 [1] CRAN (R 4.4.1)
zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
Hi,
I have tried using satuRn in a dataset for differential isoform usage on the transcript level. I really like the package, and previously it worked on another dataset for me. However, for this dataset (which is very similar to the previous one) I get an error when the algorithm is computing local FDR. I get the error:
Error in if (bett[2] > 0) bett = bet + 0.1 * solve(V, Y - mu)/(1 + 1/j^2) :
missing value where TRUE/FALSE needed
The way I understand it is that during the first time locfdr_locmle() is called, it fills the mlests with NA values, since my bett[2] is 0.77 (so if (bett[2] >= 0) {mle = rep(NA, 6)). Then the second time locfdr_locmle() is called, it tries to use the values from mlests, but these have been set to NA. Can you help me with this issue? I am not sure if this is something that I am supposed to "fix" or not, but this error feels more technical to me rather than that the input data is bad, but I do not understand the statistics behind it. I hope you can help me and I am curious if you have any insights in this.
Best wishes,
Tijs
R session information
sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.4.3 (2025-02-28)
os AlmaLinux 9.5 (Teal Serval)
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz Europe/Brussels
date 2025-04-14
rstudio 2024.12.0+467 Kousa Dogwood (server)
pandoc 3.2 @ /usr/lib/rstudio-server/bin/quarto/bin/tools/x86_64/ (via rmarkdown)
quarto 1.5.57 @ /usr/lib/rstudio-server/bin/quarto/bin/quarto
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
abind 1.4-8 2024-09-12 [1] CRAN (R 4.4.1)
annotate 1.82.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
AnnotationDbi * 1.66.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.0)
Biobase * 2.64.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocFileCache 2.12.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocGenerics * 0.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
BiocManager 1.30.25 2024-08-28 [1] CRAN (R 4.4.1)
BiocParallel * 1.38.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
biomaRt 2.60.1 2024-06-26 [1] Bioconductor 3.19 (R 4.4.1)
Biostrings 2.72.1 2024-06-02 [1] Bioconductor 3.19 (R 4.4.0)
bit 4.6.0 2025-03-06 [1] CRAN (R 4.4.3)
bit64 4.6.0-1 2025-01-16 [1] CRAN (R 4.4.3)
bitops 1.0-9 2024-10-03 [1] CRAN (R 4.4.1)
blob 1.2.4 2023-03-17 [1] CRAN (R 4.4.0)
boot 1.3-31 2024-08-28 [2] CRAN (R 4.4.3)
bslib 0.9.0 2025-01-30 [1] CRAN (R 4.4.3)
cachem 1.1.0 2024-05-16 [1] CRAN (R 4.4.0)
cli 3.6.4 2025-02-13 [1] CRAN (R 4.4.3)
codetools 0.2-20 2024-03-31 [2] CRAN (R 4.4.3)
colorspace 2.1-1 2024-07-26 [1] CRAN (R 4.4.1)
conflicted * 1.2.0 2023-02-01 [1] CRAN (R 4.4.0)
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DBI 1.2.3 2024-06-02 [1] CRAN (R 4.4.0)
dbplyr 2.5.0 2024-03-19 [1] CRAN (R 4.4.0)
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digest 0.6.37 2024-08-19 [1] CRAN (R 4.4.1)
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pbapply 1.7-2 2023-06-27 [1] CRAN (R 4.4.0)
pillar 1.10.2 2025-04-05 [1] CRAN (R 4.4.3)
pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.4.0)
png 0.1-8 2022-11-29 [1] CRAN (R 4.4.0)
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progress 1.2.3 2023-12-06 [1] CRAN (R 4.4.1)
purrr * 1.0.4 2025-02-05 [1] CRAN (R 4.4.3)
R6 2.6.1 2025-02-15 [1] CRAN (R 4.4.3)
rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.4.0)
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scales 1.3.0 2023-11-28 [1] CRAN (R 4.4.0)
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stageR 1.26.0 2024-05-01 [1] Bioconductor 3.19 (R 4.4.1)
statmod 1.5.0 2023-01-06 [1] CRAN (R 4.4.0)
stringi 1.8.7 2025-03-27 [1] CRAN (R 4.4.3)
stringr * 1.5.1 2023-11-14 [1] CRAN (R 4.4.0)
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survival 3.8-3 2024-12-17 [1] CRAN (R 4.4.3)
tibble * 3.2.1 2023-03-20 [1] CRAN (R 4.4.0)
tidyr * 1.3.1 2024-01-24 [1] CRAN (R 4.4.0)
tidyselect 1.2.1 2024-03-11 [1] CRAN (R 4.4.0)
tidyverse * 2.0.0 2023-02-22 [1] CRAN (R 4.4.0)
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UCSC.utils 1.0.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.4.0)
withr 3.0.2 2024-10-28 [1] CRAN (R 4.4.1)
xfun 0.52 2025-04-02 [1] CRAN (R 4.4.3)
XML 3.99-0.18 2025-01-01 [1] CRAN (R 4.4.3)
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zlibbioc 1.50.0 2024-04-30 [1] Bioconductor 3.19 (R 4.4.0)