benchmarks/rowsum_on_Rle_DF.md
In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining
title: "rowsum on Rle DataFrames"
author: "Charles Plessy"
date: "2023-06-30"
output:
html_document:
keep_md: yes
editor_options:
chunk_output_type: console
Purpose
There is no native rowsum function for DataFrames of Rle-encoded
numerical values. What is the best strategy for an implementation ?
Setup
library("CAGEr") |> suppressPackageStartupMessages()
library("ggplot2") |> suppressPackageStartupMessages()
The DataFrame encodes counts of CAGE tags mapped on the zebrafish genome.
# (DF <- CTSStagCountDF(exampleCAGEexp))
# DF[[1]]
#
# (names <- CTSScoordinatesGR(exampleCAGEexp)$cluster)
(DF <- ZebrafishDevelopmentalCAGE::ZebrafishCAGE |> assay())
## DataFrame with 3552111 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells zf_high
## <Rle> <Rle> <Rle> <Rle> <Rle>
## 1 0 2 0 0 0
## 2 0 0 1 0 0
## 3 0 0 0 0 0
## 4 0 0 0 0 0
## 5 0 0 0 0 0
## ... ... ... ... ... ...
## 3552107 0 0 0 1 0
## 3552108 0 0 0 0 0
## 3552109 0 0 0 0 0
## 3552110 1 0 0 0 0
## 3552111 0 0 0 0 0
## zf_oblong zf_sphere_dome zf_30perc_dome zf_shield zf_14somites zf_prim6
## <Rle> <Rle> <Rle> <Rle> <Rle> <Rle>
## 1 0 0 0 0 0 0
## 2 0 0 0 0 0 0
## 3 0 0 0 1 0 0
## 4 0 0 0 0 0 0
## 5 0 0 0 0 0 1
## ... ... ... ... ... ... ...
## 3552107 0 0 0 0 0 0
## 3552108 0 0 0 0 1 0
## 3552109 0 1 0 0 0 0
## 3552110 0 0 0 0 0 0
## 3552111 0 0 0 0 1 0
## zf_prim20
## <Rle>
## 1 0
## 2 0
## 3 0
## 4 1
## 5 2
## ... ...
## 3552107 0
## 3552108 0
## 3552109 0
## 3552110 0
## 3552111 0
DF[[1]]
## integer-Rle of length 3552111 with 796039 runs
## Lengths: 53 1 64 1 9 1 1 1 1 1 2 ... 3 1 1 3 1 33 1 78 1 1
## Values : 0 1 0 1 0 1 0 1 0 5 0 ... 0 2 1 0 2 0 1 0 1 0
# Artificial example.
(names <- rep(CTSScoordinatesGR(exampleCAGEexp)$cluster, 711)[1:nrow(DF)])
## character-Rle of length 3552111 with 571848 runs
## Lengths: 1 ... 3
## Values : "chr17:26027430:+" ... "chr17:28166212-28166.."
The functions:
.rowsumDelayedArrayAsMatrix <- function(x, group, reorder = TRUE)
rowsum(
as.matrix(DelayedArray::DelayedArray(x)),
group,
reorder = reorder) |> DataFrame()
.rowsumDelayedArrayAsMatrix(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsumDelayedArrayAsdataframe <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(DelayedArray::DelayedArray(x)),
group,
reorder = reorder) |> DataFrame()
.rowsumDelayedArrayAsdataframe(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsumDecodeAsDF <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(lapply(x, decode)),
group,
reorder = reorder) |> DataFrame()
.rowsumDecodeAsDF(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
# https://support.bioconductor.org/p/99960/#100034
.rowsum.splitAsList <- function(x, group, reorder=TRUE, ...)
lapply(x, function(col) sum(splitAsList(col, group))) |> DataFrame()
.rowsum.splitAsList(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsum.decodeSplitAsList <- function(x, group, reorder=TRUE, ...)
lapply(lapply(x, decode), function(col) sum(splitAsList(col, group))) |> DataFrame()
.rowsum.decodeSplitAsList(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
# This one I thought about after asking ChatGPT for a splitAsList alternative
.rowsum.splitAndColSums <- function(x, group, reorder=TRUE, ...) {
l <- split(x, group)
ll <- lapply(l, \(l) sapply(l, sum))
do.call(rbind, ll) |> DataFrame()
}
.rowsum.splitAndColSums(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsum.splitAndColSums(endoapply(DF, decode), decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
Benchmark
(microbench_out <- microbenchmark::microbenchmark(
times = 100,
.rowsumDelayedArrayAsMatrix = .rowsumDelayedArrayAsMatrix(DF, decode(names), reorder = FALSE),
.rowsumDelayedArrayAsdataframe = .rowsumDelayedArrayAsdataframe(DF, decode(names), reorder = FALSE),
.rowsumDecodeAsDF = .rowsumDecodeAsDF(DF, decode(names), reorder = FALSE),
.rowsum.splitAsList = .rowsum.splitAsList(DF, decode(names), reorder = FALSE),
.rowsum.decodeSplitAsList = .rowsum.decodeSplitAsList(DF, decode(names), reorder = FALSE) #,
# Interesting, # .rowsum.splitAndColSums = .rowsum.splitAndColSums(DF, decode(names), reorder = FALSE),
# but too slow # .rowsum.DecodeSplitAndColSums = .rowsum.splitAndColSums(endoapply(DF, decode), decode(names), reorder = FALSE)
))
## Unit: milliseconds
## expr min lq mean median
## .rowsumDelayedArrayAsMatrix 670.0519 767.4457 1095.5916 882.0108
## .rowsumDelayedArrayAsdataframe 835.3315 982.0086 1335.5997 1561.0492
## .rowsumDecodeAsDF 498.6539 509.8449 556.0318 513.3068
## .rowsum.splitAsList 4916.0498 4964.3569 5126.3069 5013.1646
## .rowsum.decodeSplitAsList 2133.9391 2185.7487 2600.7488 2624.4384
## uq max neval
## 1491.9984 1691.589 100
## 1668.5892 1902.639 100
## 528.9106 1273.422 100
## 5080.1585 5973.912 100
## 2962.9610 3661.528 100
# https://statisticsglobe.com/microbenchmark-package-r
ggplot(microbench_out, aes(x = time / 1e9, y = expr, color = expr)) + # Plot performance comparison
geom_boxplot() +
scale_x_log10("time (seconds)")
Result
The winner is:
.rowsumDecodeAsDF <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(lapply(x, decode)),
group,
reorder = reorder) |> DataFrame()
Needless to say, the reorder argument needs to be implemented with care.
Session information
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 12 (bookworm)
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ggplot2_3.4.2 CAGEr_2.6.0
## [3] MultiAssayExperiment_1.26.0 SummarizedExperiment_1.30.2
## [5] Biobase_2.60.0 GenomicRanges_1.52.0
## [7] GenomeInfoDb_1.36.1 IRanges_2.34.1
## [9] S4Vectors_0.38.1 BiocGenerics_0.46.0
## [11] MatrixGenerics_1.12.2 matrixStats_1.0.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.14
## [3] jsonlite_1.8.5 magrittr_2.0.3
## [5] GenomicFeatures_1.52.1 farver_2.1.1
## [7] rmarkdown_2.22 BiocIO_1.10.0
## [9] zlibbioc_1.46.0 vctrs_0.6.2
## [11] memoise_2.0.1 Rsamtools_2.16.0
## [13] DelayedMatrixStats_1.22.1 RCurl_1.98-1.12
## [15] base64enc_0.1-3 htmltools_0.5.5
## [17] S4Arrays_1.0.4 progress_1.2.2
## [19] curl_5.0.1 Formula_1.2-5
## [21] sass_0.4.6 KernSmooth_2.23-20
## [23] bslib_0.5.0 htmlwidgets_1.6.2
## [25] plyr_1.8.8 Gviz_1.44.0
## [27] cachem_1.0.8 GenomicAlignments_1.36.0
## [29] lifecycle_1.0.3 pkgconfig_2.0.3
## [31] Matrix_1.5-3 R6_2.5.1
## [33] fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [35] digest_0.6.31 colorspace_2.1-0
## [37] AnnotationDbi_1.62.1 Hmisc_5.1-0
## [39] RSQLite_2.3.1 vegan_2.6-4
## [41] filelock_1.0.2 fansi_1.0.4
## [43] mgcv_1.8-41 httr_1.4.6
## [45] compiler_4.3.0 microbenchmark_1.4.10
## [47] withr_2.5.0 bit64_4.0.5
## [49] htmlTable_2.4.1 backports_1.4.1
## [51] CAGEfightR_1.20.0 BiocParallel_1.34.2
## [53] DBI_1.1.3 highr_0.10
## [55] biomaRt_2.56.1 MASS_7.3-58.2
## [57] rappdirs_0.3.3 DelayedArray_0.26.4
## [59] rjson_0.2.21 permute_0.9-7
## [61] gtools_3.9.4 tools_4.3.0
## [63] foreign_0.8-84 nnet_7.3-18
## [65] glue_1.6.2 restfulr_0.0.15
## [67] nlme_3.1-162 stringdist_0.9.10
## [69] grid_4.3.0 checkmate_2.2.0
## [71] reshape2_1.4.4 cluster_2.1.4
## [73] generics_0.1.3 operator.tools_1.6.3
## [75] gtable_0.3.3 BSgenome_1.68.0
## [77] formula.tools_1.7.1 ensembldb_2.24.0
## [79] ZebrafishDevelopmentalCAGE_0.999.0 data.table_1.14.8
## [81] hms_1.1.3 xml2_1.3.4
## [83] utf8_1.2.3 XVector_0.40.0
## [85] pillar_1.9.0 stringr_1.5.0
## [87] splines_4.3.0 dplyr_1.1.2
## [89] BiocFileCache_2.8.0 lattice_0.20-45
## [91] rtracklayer_1.60.0 bit_4.0.5
## [93] deldir_1.0-9 biovizBase_1.48.0
## [95] tidyselect_1.2.0 Biostrings_2.68.1
## [97] knitr_1.43 gridExtra_2.3
## [99] ProtGenerics_1.32.0 xfun_0.39
## [101] stringi_1.7.12 VGAM_1.1-8
## [103] lazyeval_0.2.2 yaml_2.3.7
## [105] som_0.3-5.1 evaluate_0.21
## [107] codetools_0.2-19 interp_1.1-4
## [109] tibble_3.2.1 cli_3.6.1
## [111] rpart_4.1.19 munsell_0.5.0
## [113] jquerylib_0.1.4 dichromat_2.0-0.1
## [115] Rcpp_1.0.10 dbplyr_2.3.2
## [117] png_0.1-8 XML_3.99-0.14
## [119] parallel_4.3.0 assertthat_0.2.1
## [121] blob_1.2.4 prettyunits_1.1.1
## [123] latticeExtra_0.6-30 jpeg_0.1-10
## [125] AnnotationFilter_1.24.0 sparseMatrixStats_1.12.1
## [127] bitops_1.0-7 VariantAnnotation_1.46.0
## [129] scales_1.2.1 crayon_1.5.2
## [131] rlang_1.1.1 KEGGREST_1.40.0
ChatGPT
Charles Plessy 7:52 PM
Good evening ChatGPT, can you tell me an alternative to the Bioconductor function splitAsList ?
Sidekick APP 7:52 PM
An alternative to the splitAsList function from Bioconductor in R could be the combination of the split and as.list functions from base R. Here's an example:
r
# Assuming 'df' is your data frame and 'group' is the column you want to split by
split_list = as.list(split(df, df$group))
This will give you a list of data frames, split by the 'group' column, similar to what splitAsList would do.
charles-plessy/CAGEr documentation built on Oct. 27, 2024, 10:11 p.m.
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title: "rowsum on Rle DataFrames" author: "Charles Plessy" date: "2023-06-30" output: html_document: keep_md: yes editor_options: chunk_output_type: console
Purpose
There is no native rowsum function for DataFrames of Rle-encoded
numerical values. What is the best strategy for an implementation ?
Setup
library("CAGEr") |> suppressPackageStartupMessages()
library("ggplot2") |> suppressPackageStartupMessages()
The DataFrame encodes counts of CAGE tags mapped on the zebrafish genome.
# (DF <- CTSStagCountDF(exampleCAGEexp))
# DF[[1]]
#
# (names <- CTSScoordinatesGR(exampleCAGEexp)$cluster)
(DF <- ZebrafishDevelopmentalCAGE::ZebrafishCAGE |> assay())
## DataFrame with 3552111 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells zf_high
## <Rle> <Rle> <Rle> <Rle> <Rle>
## 1 0 2 0 0 0
## 2 0 0 1 0 0
## 3 0 0 0 0 0
## 4 0 0 0 0 0
## 5 0 0 0 0 0
## ... ... ... ... ... ...
## 3552107 0 0 0 1 0
## 3552108 0 0 0 0 0
## 3552109 0 0 0 0 0
## 3552110 1 0 0 0 0
## 3552111 0 0 0 0 0
## zf_oblong zf_sphere_dome zf_30perc_dome zf_shield zf_14somites zf_prim6
## <Rle> <Rle> <Rle> <Rle> <Rle> <Rle>
## 1 0 0 0 0 0 0
## 2 0 0 0 0 0 0
## 3 0 0 0 1 0 0
## 4 0 0 0 0 0 0
## 5 0 0 0 0 0 1
## ... ... ... ... ... ... ...
## 3552107 0 0 0 0 0 0
## 3552108 0 0 0 0 1 0
## 3552109 0 1 0 0 0 0
## 3552110 0 0 0 0 0 0
## 3552111 0 0 0 0 1 0
## zf_prim20
## <Rle>
## 1 0
## 2 0
## 3 0
## 4 1
## 5 2
## ... ...
## 3552107 0
## 3552108 0
## 3552109 0
## 3552110 0
## 3552111 0
DF[[1]]
## integer-Rle of length 3552111 with 796039 runs
## Lengths: 53 1 64 1 9 1 1 1 1 1 2 ... 3 1 1 3 1 33 1 78 1 1
## Values : 0 1 0 1 0 1 0 1 0 5 0 ... 0 2 1 0 2 0 1 0 1 0
# Artificial example.
(names <- rep(CTSScoordinatesGR(exampleCAGEexp)$cluster, 711)[1:nrow(DF)])
## character-Rle of length 3552111 with 571848 runs
## Lengths: 1 ... 3
## Values : "chr17:26027430:+" ... "chr17:28166212-28166.."
The functions:
.rowsumDelayedArrayAsMatrix <- function(x, group, reorder = TRUE)
rowsum(
as.matrix(DelayedArray::DelayedArray(x)),
group,
reorder = reorder) |> DataFrame()
.rowsumDelayedArrayAsMatrix(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsumDelayedArrayAsdataframe <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(DelayedArray::DelayedArray(x)),
group,
reorder = reorder) |> DataFrame()
.rowsumDelayedArrayAsdataframe(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsumDecodeAsDF <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(lapply(x, decode)),
group,
reorder = reorder) |> DataFrame()
.rowsumDecodeAsDF(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
# https://support.bioconductor.org/p/99960/#100034
.rowsum.splitAsList <- function(x, group, reorder=TRUE, ...)
lapply(x, function(col) sum(splitAsList(col, group))) |> DataFrame()
.rowsum.splitAsList(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsum.decodeSplitAsList <- function(x, group, reorder=TRUE, ...)
lapply(lapply(x, decode), function(col) sum(splitAsList(col, group))) |> DataFrame()
.rowsum.decodeSplitAsList(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
# This one I thought about after asking ChatGPT for a splitAsList alternative
.rowsum.splitAndColSums <- function(x, group, reorder=TRUE, ...) {
l <- split(x, group)
ll <- lapply(l, \(l) sapply(l, sum))
do.call(rbind, ll) |> DataFrame()
}
.rowsum.splitAndColSums(DF, decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
.rowsum.splitAndColSums(endoapply(DF, decode), decode(names), reorder = FALSE) |> head()
## DataFrame with 6 rows and 12 columns
## zf_unfertilized_egg zf_fertilized_egg zf_64cells zf_512cells
## <integer> <integer> <integer> <integer>
## chr17:26027430:+ 418 572 512 473
## chr17:26050540:+ 484 762 1137 1141
## chr17:26118088:+ 530 619 937 824
## chr17:26142853:+ 494 607 647 652
## chr17:26166954:+ 491 520 610 512
## chr17:26222417:+ 326 414 1015 785
## zf_high zf_oblong zf_sphere_dome zf_30perc_dome zf_shield
## <integer> <integer> <integer> <integer> <integer>
## chr17:26027430:+ 461 392 373 386 152
## chr17:26050540:+ 627 733 763 805 364
## chr17:26118088:+ 588 615 588 651 246
## chr17:26142853:+ 622 513 452 526 190
## chr17:26166954:+ 454 419 725 777 355
## chr17:26222417:+ 454 392 513 547 242
## zf_14somites zf_prim6 zf_prim20
## <integer> <integer> <integer>
## chr17:26027430:+ 550 617 433
## chr17:26050540:+ 1573 1335 1055
## chr17:26118088:+ 1251 2319 1054
## chr17:26142853:+ 1297 952 762
## chr17:26166954:+ 941 932 814
## chr17:26222417:+ 1240 4282 939
Benchmark
(microbench_out <- microbenchmark::microbenchmark(
times = 100,
.rowsumDelayedArrayAsMatrix = .rowsumDelayedArrayAsMatrix(DF, decode(names), reorder = FALSE),
.rowsumDelayedArrayAsdataframe = .rowsumDelayedArrayAsdataframe(DF, decode(names), reorder = FALSE),
.rowsumDecodeAsDF = .rowsumDecodeAsDF(DF, decode(names), reorder = FALSE),
.rowsum.splitAsList = .rowsum.splitAsList(DF, decode(names), reorder = FALSE),
.rowsum.decodeSplitAsList = .rowsum.decodeSplitAsList(DF, decode(names), reorder = FALSE) #,
# Interesting, # .rowsum.splitAndColSums = .rowsum.splitAndColSums(DF, decode(names), reorder = FALSE),
# but too slow # .rowsum.DecodeSplitAndColSums = .rowsum.splitAndColSums(endoapply(DF, decode), decode(names), reorder = FALSE)
))
## Unit: milliseconds
## expr min lq mean median
## .rowsumDelayedArrayAsMatrix 670.0519 767.4457 1095.5916 882.0108
## .rowsumDelayedArrayAsdataframe 835.3315 982.0086 1335.5997 1561.0492
## .rowsumDecodeAsDF 498.6539 509.8449 556.0318 513.3068
## .rowsum.splitAsList 4916.0498 4964.3569 5126.3069 5013.1646
## .rowsum.decodeSplitAsList 2133.9391 2185.7487 2600.7488 2624.4384
## uq max neval
## 1491.9984 1691.589 100
## 1668.5892 1902.639 100
## 528.9106 1273.422 100
## 5080.1585 5973.912 100
## 2962.9610 3661.528 100
# https://statisticsglobe.com/microbenchmark-package-r
ggplot(microbench_out, aes(x = time / 1e9, y = expr, color = expr)) + # Plot performance comparison
geom_boxplot() +
scale_x_log10("time (seconds)")
Result
The winner is:
.rowsumDecodeAsDF <- function(x, group, reorder = TRUE)
rowsum(
as.data.frame(lapply(x, decode)),
group,
reorder = reorder) |> DataFrame()
Needless to say, the reorder argument needs to be implemented with care.
Session information
sessionInfo()
## R version 4.3.0 (2023-04-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 12 (bookworm)
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] ggplot2_3.4.2 CAGEr_2.6.0
## [3] MultiAssayExperiment_1.26.0 SummarizedExperiment_1.30.2
## [5] Biobase_2.60.0 GenomicRanges_1.52.0
## [7] GenomeInfoDb_1.36.1 IRanges_2.34.1
## [9] S4Vectors_0.38.1 BiocGenerics_0.46.0
## [11] MatrixGenerics_1.12.2 matrixStats_1.0.0
##
## loaded via a namespace (and not attached):
## [1] RColorBrewer_1.1-3 rstudioapi_0.14
## [3] jsonlite_1.8.5 magrittr_2.0.3
## [5] GenomicFeatures_1.52.1 farver_2.1.1
## [7] rmarkdown_2.22 BiocIO_1.10.0
## [9] zlibbioc_1.46.0 vctrs_0.6.2
## [11] memoise_2.0.1 Rsamtools_2.16.0
## [13] DelayedMatrixStats_1.22.1 RCurl_1.98-1.12
## [15] base64enc_0.1-3 htmltools_0.5.5
## [17] S4Arrays_1.0.4 progress_1.2.2
## [19] curl_5.0.1 Formula_1.2-5
## [21] sass_0.4.6 KernSmooth_2.23-20
## [23] bslib_0.5.0 htmlwidgets_1.6.2
## [25] plyr_1.8.8 Gviz_1.44.0
## [27] cachem_1.0.8 GenomicAlignments_1.36.0
## [29] lifecycle_1.0.3 pkgconfig_2.0.3
## [31] Matrix_1.5-3 R6_2.5.1
## [33] fastmap_1.1.1 GenomeInfoDbData_1.2.10
## [35] digest_0.6.31 colorspace_2.1-0
## [37] AnnotationDbi_1.62.1 Hmisc_5.1-0
## [39] RSQLite_2.3.1 vegan_2.6-4
## [41] filelock_1.0.2 fansi_1.0.4
## [43] mgcv_1.8-41 httr_1.4.6
## [45] compiler_4.3.0 microbenchmark_1.4.10
## [47] withr_2.5.0 bit64_4.0.5
## [49] htmlTable_2.4.1 backports_1.4.1
## [51] CAGEfightR_1.20.0 BiocParallel_1.34.2
## [53] DBI_1.1.3 highr_0.10
## [55] biomaRt_2.56.1 MASS_7.3-58.2
## [57] rappdirs_0.3.3 DelayedArray_0.26.4
## [59] rjson_0.2.21 permute_0.9-7
## [61] gtools_3.9.4 tools_4.3.0
## [63] foreign_0.8-84 nnet_7.3-18
## [65] glue_1.6.2 restfulr_0.0.15
## [67] nlme_3.1-162 stringdist_0.9.10
## [69] grid_4.3.0 checkmate_2.2.0
## [71] reshape2_1.4.4 cluster_2.1.4
## [73] generics_0.1.3 operator.tools_1.6.3
## [75] gtable_0.3.3 BSgenome_1.68.0
## [77] formula.tools_1.7.1 ensembldb_2.24.0
## [79] ZebrafishDevelopmentalCAGE_0.999.0 data.table_1.14.8
## [81] hms_1.1.3 xml2_1.3.4
## [83] utf8_1.2.3 XVector_0.40.0
## [85] pillar_1.9.0 stringr_1.5.0
## [87] splines_4.3.0 dplyr_1.1.2
## [89] BiocFileCache_2.8.0 lattice_0.20-45
## [91] rtracklayer_1.60.0 bit_4.0.5
## [93] deldir_1.0-9 biovizBase_1.48.0
## [95] tidyselect_1.2.0 Biostrings_2.68.1
## [97] knitr_1.43 gridExtra_2.3
## [99] ProtGenerics_1.32.0 xfun_0.39
## [101] stringi_1.7.12 VGAM_1.1-8
## [103] lazyeval_0.2.2 yaml_2.3.7
## [105] som_0.3-5.1 evaluate_0.21
## [107] codetools_0.2-19 interp_1.1-4
## [109] tibble_3.2.1 cli_3.6.1
## [111] rpart_4.1.19 munsell_0.5.0
## [113] jquerylib_0.1.4 dichromat_2.0-0.1
## [115] Rcpp_1.0.10 dbplyr_2.3.2
## [117] png_0.1-8 XML_3.99-0.14
## [119] parallel_4.3.0 assertthat_0.2.1
## [121] blob_1.2.4 prettyunits_1.1.1
## [123] latticeExtra_0.6-30 jpeg_0.1-10
## [125] AnnotationFilter_1.24.0 sparseMatrixStats_1.12.1
## [127] bitops_1.0-7 VariantAnnotation_1.46.0
## [129] scales_1.2.1 crayon_1.5.2
## [131] rlang_1.1.1 KEGGREST_1.40.0
ChatGPT
Charles Plessy 7:52 PM
Good evening ChatGPT, can you tell me an alternative to the Bioconductor function
splitAsList?
Sidekick APP 7:52 PM
An alternative to the
splitAsListfunction from Bioconductor in R could be the combination of thesplitandas.listfunctions from base R. Here's an example:
r
# Assuming 'df' is your data frame and 'group' is the column you want to split by
split_list = as.list(split(df, df$group))
This will give you a list of data frames, split by the 'group' column, similar to what
splitAsListwould do.
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