In this vignette, we demonstrate the unsegmented block bootstrap functionality implemented in nullranges. “Unsegmented” refers to the fact that this implementation does not consider segmentation of the genome for sampling of blocks, see the segmented block bootstrap vignette for the alternative implementation.
First we use the DNase hypersensitivity peaks in A549 downloaded from AnnotationHub, and pre-processed as described in the nullrangesOldData package.
## see ?nullrangesData and browseVignettes('nullrangesData') for documentation
## loading from cache
The following chunk of code evaluates various types of bootstrap/permutation schemes, first within chromosome, and then across chromosome (the default). The default type
is bootstrap, and the default for withinChrom
is FALSE
(bootstrapping with blocks moving across chromosomes).
set.seed(5) # reproducibility
library(microbenchmark)
blockLength <- 5e5
microbenchmark(
list=alist(
p_within=bootRanges(dhs, blockLength=blockLength,
type="permute", withinChrom=TRUE),
b_within=bootRanges(dhs, blockLength=blockLength,
type="bootstrap", withinChrom=TRUE),
p_across=bootRanges(dhs, blockLength=blockLength,
type="permute", withinChrom=FALSE),
b_across=bootRanges(dhs, blockLength=blockLength,
type="bootstrap", withinChrom=FALSE)
), times=10)
## Unit: milliseconds
## expr min lq mean median uq max neval cld
## p_within 1924.7292 2114.1387 3232.5426 3461.7118 4292.8154 4323.8642 10 b
## b_within 1496.6154 1802.3284 2616.8213 2425.7709 3614.1810 3837.6499 10 b
## p_across 323.7575 355.0375 480.9807 391.9079 505.4548 989.2774 10 a
## b_across 424.1389 501.6898 599.5443 636.7258 672.4426 777.1074 10 a
We create some synthetic ranges in order to visualize the different options of the unsegmented bootstrap implemented in nullranges.
library(GenomicRanges)
seq_nms <- rep(c("chr1","chr2","chr3"),c(4,5,2))
gr <- GRanges(seqnames=seq_nms,
IRanges(start=c(1,101,121,201,
101,201,216,231,401,
1,101),
width=c(20, 5, 5, 30,
20, 5, 5, 5, 30,
80, 40)),
seqlengths=c(chr1=300,chr2=450,chr3=200),
chr=factor(seq_nms))
The following function uses functionality from plotgardener to plot the ranges. Note in the plotting helper function that chr
will be used to color ranges by chromosome of origin.
suppressPackageStartupMessages(library(plotgardener))
plotGRanges <- function(gr) {
pageCreate(width = 5, height = 2, xgrid = 0,
ygrid = 0, showGuides = FALSE)
for (i in seq_along(seqlevels(gr))) {
chrom <- seqlevels(gr)[i]
chromend <- seqlengths(gr)[[chrom]]
suppressMessages({
p <- pgParams(chromstart = 0, chromend = chromend,
x = 0.5, width = 4*chromend/500, height = 0.5,
at = seq(0, chromend, 50),
fill = colorby("chr", palette=palette.colors))
prngs <- plotRanges(data = gr, params = p,
chrom = chrom,
y = 0.25 + (i-1)*.7,
just = c("left", "bottom"))
annoGenomeLabel(plot = prngs, params = p, y = 0.30 + (i-1)*.7)
})
}
}
Visualizing two permutations of blocks within chromosome:
for (i in 1:2) {
gr_prime <- bootRanges(gr, blockLength=100, type="permute", withinChrom=TRUE)
plotGRanges(gr_prime)
}
Visualizing two bootstraps within chromosome:
for (i in 1:2) {
gr_prime <- bootRanges(gr, blockLength=100, withinChrom=TRUE)
plotGRanges(gr_prime)
}
Visualizing two permutations of blocks across chromosome. Here we use larger blocks than previously.
for (i in 1:2) {
gr_prime <- bootRanges(gr, blockLength=200, type="permute", withinChrom=FALSE)
plotGRanges(gr_prime)
}
Visualizing two bootstraps across chromosome:
for (i in 1:2) {
gr_prime <- bootRanges(gr, blockLength=200, withinChrom=FALSE)
plotGRanges(gr_prime)
}
## R version 4.1.1 Patched (2021-08-22 r80813)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Mojave 10.14.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] grid stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] microbenchmark_1.4-7 excluderanges_0.99.6
## [3] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.18.0
## [5] AnnotationFilter_1.18.0 GenomicFeatures_1.46.0
## [7] AnnotationDbi_1.56.0 patchwork_1.1.1
## [9] plyranges_1.14.0 nullrangesData_0.99.2
## [11] ExperimentHub_2.2.0 AnnotationHub_3.2.0
## [13] BiocFileCache_2.2.0 dbplyr_2.1.1
## [15] ggplot2_3.3.5 plotgardener_1.0.0
## [17] nullranges_1.0.0 InteractionSet_1.22.0
## [19] SummarizedExperiment_1.24.0 Biobase_2.54.0
## [21] MatrixGenerics_1.6.0 matrixStats_0.61.0
## [23] GenomicRanges_1.46.0 GenomeInfoDb_1.30.0
## [25] IRanges_2.28.0 S4Vectors_0.32.0
## [27] BiocGenerics_0.40.0
##
## loaded via a namespace (and not attached):
## [1] plyr_1.8.6 RcppHMM_1.2.2
## [3] lazyeval_0.2.2 splines_4.1.1
## [5] BiocParallel_1.28.0 TH.data_1.1-0
## [7] digest_0.6.28 yulab.utils_0.0.4
## [9] htmltools_0.5.2 fansi_0.5.0
## [11] magrittr_2.0.1 memoise_2.0.0
## [13] ks_1.13.2 Biostrings_2.62.0
## [15] sandwich_3.0-1 prettyunits_1.1.1
## [17] colorspace_2.0-2 blob_1.2.2
## [19] rappdirs_0.3.3 xfun_0.27
## [21] dplyr_1.0.7 crayon_1.4.1
## [23] RCurl_1.98-1.5 jsonlite_1.7.2
## [25] survival_3.2-13 zoo_1.8-9
## [27] glue_1.4.2 gtable_0.3.0
## [29] zlibbioc_1.40.0 XVector_0.34.0
## [31] strawr_0.0.9 DelayedArray_0.20.0
## [33] scales_1.1.1 mvtnorm_1.1-3
## [35] DBI_1.1.1 Rcpp_1.0.7
## [37] xtable_1.8-4 progress_1.2.2
## [39] gridGraphics_0.5-1 bit_4.0.4
## [41] mclust_5.4.7 httr_1.4.2
## [43] RColorBrewer_1.1-2 speedglm_0.3-3
## [45] ellipsis_0.3.2 pkgconfig_2.0.3
## [47] XML_3.99-0.8 farver_2.1.0
## [49] sass_0.4.0 utf8_1.2.2
## [51] DNAcopy_1.68.0 ggplotify_0.1.0
## [53] tidyselect_1.1.1 labeling_0.4.2
## [55] rlang_0.4.12 later_1.3.0
## [57] munsell_0.5.0 BiocVersion_3.14.0
## [59] tools_4.1.1 cachem_1.0.6
## [61] generics_0.1.1 RSQLite_2.2.8
## [63] ggridges_0.5.3 evaluate_0.14
## [65] stringr_1.4.0 fastmap_1.1.0
## [67] yaml_2.2.1 knitr_1.36
## [69] bit64_4.0.5 purrr_0.3.4
## [71] KEGGREST_1.34.0 mime_0.12
## [73] pracma_2.3.3 xml2_1.3.2
## [75] biomaRt_2.50.0 compiler_4.1.1
## [77] filelock_1.0.2 curl_4.3.2
## [79] png_0.1-7 interactiveDisplayBase_1.32.0
## [81] tibble_3.1.5 bslib_0.3.1
## [83] stringi_1.7.5 highr_0.9
## [85] lattice_0.20-45 ProtGenerics_1.26.0
## [87] Matrix_1.3-4 vctrs_0.3.8
## [89] pillar_1.6.4 lifecycle_1.0.1
## [91] BiocManager_1.30.16 jquerylib_0.1.4
## [93] data.table_1.14.2 bitops_1.0-7
## [95] httpuv_1.6.3 rtracklayer_1.54.0
## [97] R6_2.5.1 BiocIO_1.4.0
## [99] promises_1.2.0.1 KernSmooth_2.23-20
## [101] codetools_0.2-18 MASS_7.3-54
## [103] assertthat_0.2.1 rjson_0.2.20
## [105] withr_2.4.2 GenomicAlignments_1.30.0
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