Exploratory MITOBREAK and Orlov’s data analysis
Last updated: 2023-04-05
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Knit directory: GlobalStructure/
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1: READ MITOBREAK AND KEEP ONLY MAJOR ARC DELETIONS:
breaks <- read.table(
here(
raw_dir,
"MitoBreakDB_12122019.csv"),
sep = ',',
header = TRUE)
breaks$X5..breakpoint <-
as.numeric(as.character(breaks$X5..breakpoint))
summary(breaks$X5..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
83 6165 7668 7135 8562 16266 1 breaks$X3..breakpoint <-
as.numeric(as.character(breaks$X3..breakpoint))
summary(breaks$X3..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
24 13787 15075 14349 16035 16599 1 breaks <- breaks[!is.na(breaks$X3..breakpoint) &
!is.na(breaks$X5..breakpoint),]par(mfrow = c(2, 1))
hist(breaks$X5..breakpoint, breaks = seq(0, 16600, 100))
hist(breaks$X3..breakpoint, breaks = seq(0, 16600, 100))
nrow(breaks)[1] 1312breaks = breaks[breaks$Deletion.of.replication.origins == 'None', ]
nrow(breaks)[1] 1110breaks = breaks[breaks$Location.of.the.deleted.region == 'Inside the major arc', ]
nrow(breaks)[1] 1082summary(breaks$X5..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
105 7117 7976 8063 8661 16164 summary(breaks$X3..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
24 13801 15078 14551 16006 16599 hist(breaks$X5..breakpoint, breaks = seq(0, 16600, 100))
hist(breaks$X3..breakpoint, breaks = seq(0, 16600, 100))
# OH: 110-441
# OL: 5721-5781
for (i in 1:nrow(breaks))
{
if (breaks$X5..breakpoint[i] < 110) {
breaks$X5..breakpoint[i] = breaks$X5..breakpoint[i] + 16569
}
if (breaks$X3..breakpoint[i] < 110) {
breaks$X3..breakpoint[i] = breaks$X3..breakpoint[i] + 16569
}
}
summary(breaks$X5..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
306 7119 7980 8078 8662 16674 summary(breaks$X3..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
112 13806 15109 14581 16030 16654 nrow(breaks)[1] 1082breaks = breaks[breaks$X5..breakpoint > 5781 &
breaks$X3..breakpoint > 5781, ]
nrow(breaks)[1] 1060summary(breaks$X5..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
5782 7127 7980 8097 8663 16164 summary(breaks$X3..breakpoint) Min. 1st Qu. Median Mean 3rd Qu. Max.
6025 13826 15145 14741 16035 16654 hist(breaks$X5..breakpoint, breaks = seq(0, 16700, 100))
hist(breaks$X3..breakpoint, breaks = seq(0, 16700, 100))
2: read Orlovs’s direct perfect repeats
Rep <- read.table(
here(raw_dir, "Homo_sapiens.input.out4out.SecondPart"),
header = TRUE,
sep = '\t'
) # 767
Rep <- Rep[Rep$RepName == 'Direct_repeat', ] # 330
Rep$RepStart <- as.numeric(as.character(Rep$RepStart))
Rep$RepEnd <- as.numeric(as.character(Rep$RepEnd))
Rep <- Rep[Rep$RepStart > 5781 &
Rep$RepStart < 16569 &
Rep$RepEnd > 5781 & Rep$RepEnd < 16569, ] # 1713: plot repeats and breakpoints
par(mfrow=c(1,1))
plot(breaks$X5..breakpoint,breaks$X3..breakpoint,xlim = c(5781,16569), ylim=c(16569,5781), col = rgb(0.5,0.5,0.5,0.2), pch = 16, xlab = '5\'breakpoint', ylab = '3\'breakpoint')
par(new= TRUE)
plot(Rep$RepEnd,Rep$RepStart, xlim = c(5781,16569), ylim=c(16569,5781), col = rgb(1,0.1,0.1,0.5), pch = 16, xlab = '5\'breakpoint', ylab = '3\'breakpoint')
legend(12000, 8000, c('deletions','repeats'), col=c(rgb(0.5,0.5,0.5,0.5),rgb(1,0.1,0.1,0.5)), pch = 16)
sessionInfo()R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
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
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] here_1.0.1 lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0
[5] dplyr_1.1.1 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0
[9] tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] tidyselect_1.2.0 xfun_0.38 bslib_0.4.2 colorspace_2.1-0
[5] vctrs_0.6.1 generics_0.1.3 htmltools_0.5.5 yaml_2.3.7
[9] utf8_1.2.3 rlang_1.1.0 jquerylib_0.1.4 later_1.3.0
[13] pillar_1.9.0 glue_1.6.2 withr_2.5.0 lifecycle_1.0.3
[17] munsell_0.5.0 gtable_0.3.3 evaluate_0.20 knitr_1.42
[21] tzdb_0.3.0 callr_3.7.3 fastmap_1.1.1 httpuv_1.6.9
[25] ps_1.7.4 fansi_1.0.4 highr_0.10 Rcpp_1.0.10
[29] renv_0.17.2 promises_1.2.0.1 scales_1.2.1 cachem_1.0.7
[33] jsonlite_1.8.4 fs_1.6.1 hms_1.1.3 digest_0.6.31
[37] stringi_1.7.12 processx_3.8.0 getPass_0.2-2 rprojroot_2.0.3
[41] grid_4.2.2 cli_3.6.1 tools_4.2.2 magrittr_2.0.3
[45] sass_0.4.5 whisker_0.4.1 pkgconfig_2.0.3 timechange_0.2.0
[49] rmarkdown_2.21 httr_1.4.5 rstudioapi_0.14 R6_2.5.1
[53] git2r_0.31.0 compiler_4.2.2