1 Main libraries and configuration
library(dplyr)
library(GenomicRanges)
pathDropbox <- file.path(dir("~", pattern = "Dropbox", full.names = TRUE))
setwd(file.path(pathDropbox,"coMethDMR_metaAnalysis/overlapWithDNA"))library(dplyr)
library(GenomicRanges)
pathDropbox <- file.path(dir("~", pattern = "Dropbox", full.names = TRUE))
setwd(file.path(pathDropbox,"coMethDMR_metaAnalysis/overlapWithDNA"))SNPregions <- read.csv("AD_SNPregions.csv")
SNPregions <- subset (SNPregions, select = -c(LDchr500, LDstart500kb, LDend500kb) )
sigCpGs <- read.csv("AD_sigCpGs.csv")
SNPregions_ranges <- GRanges(
seqnames = SNPregions$LDchr,
ranges = IRanges(SNPregions$LDstart, SNPregions$LDend)
)
sigCpGs_ranges <- GRanges(
seqnames = sigCpGs$chr,
ranges = IRanges(sigCpGs$start, sigCpGs$end)
)
overlap <- findOverlaps(SNPregions_ranges, sigCpGs_ranges)
overlap_df <- as.data.frame(overlap)
SNPsOverlap <- SNPregions[overlap_df$queryHits,]
sigCpGsOverlap <- sigCpGs[overlap_df$subjectHits,]
SNPsigCpGsOverlap <- cbind(SNPsOverlap, sigCpGsOverlap)
SNPsigCpGsOverlapwrite.csv(SNPsigCpGsOverlap,
"AD_SNPs_sigCpGs_overlap.csv",
row.names = FALSE)devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R Under development (unstable) (2020-02-25 r77857)
## os macOS Catalina 10.15.3
## system x86_64, darwin15.6.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/New_York
## date 2020-04-26
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## package * version date lib
## assertthat 0.2.1 2019-03-21 [1]
## backports 1.1.6 2020-04-05 [1]
## base64enc 0.1-3 2015-07-28 [1]
## BiocGenerics * 0.33.3 2020-03-23 [1]
## bitops 1.0-6 2013-08-17 [1]
## callr 3.4.3 2020-03-28 [1]
## cli 2.0.2 2020-02-28 [1]
## crayon 1.3.4 2017-09-16 [1]
## desc 1.2.0 2018-05-01 [1]
## devtools 2.3.0 2020-04-10 [1]
## digest 0.6.25 2020-02-23 [1]
## dplyr * 0.8.99.9002 2020-04-02 [1]
## ellipsis 0.3.0 2019-09-20 [1]
## evaluate 0.14 2019-05-28 [1]
## fansi 0.4.1 2020-01-08 [1]
## fs 1.4.1 2020-04-04 [1]
## generics 0.0.2 2018-11-29 [1]
## GenomeInfoDb * 1.23.17 2020-04-13 [1]
## GenomeInfoDbData 1.2.3 2020-04-20 [1]
## GenomicRanges * 1.39.3 2020-04-08 [1]
## glue 1.4.0 2020-04-03 [1]
## htmltools 0.4.0 2019-10-04 [1]
## IRanges * 2.21.8 2020-03-25 [1]
## jsonlite 1.6.1 2020-02-02 [1]
## knitr 1.28 2020-02-06 [1]
## lifecycle 0.2.0 2020-03-06 [1]
## magrittr 1.5 2014-11-22 [1]
## memoise 1.1.0 2017-04-21 [1]
## pillar 1.4.3 2019-12-20 [1]
## pkgbuild 1.0.6 2019-10-09 [1]
## pkgconfig 2.0.3 2019-09-22 [1]
## pkgload 1.0.2 2018-10-29 [1]
## prettyunits 1.1.1 2020-01-24 [1]
## processx 3.4.2 2020-02-09 [1]
## ps 1.3.2 2020-02-13 [1]
## purrr 0.3.4 2020-04-17 [1]
## R6 2.4.1 2019-11-12 [1]
## Rcpp 1.0.4.6 2020-04-09 [1]
## RCurl 1.98-1.2 2020-04-18 [1]
## remotes 2.1.1 2020-02-15 [1]
## rlang 0.4.5.9000 2020-03-20 [1]
## rmarkdown 2.1 2020-01-20 [1]
## rprojroot 1.3-2 2018-01-03 [1]
## S4Vectors * 0.25.15 2020-04-04 [1]
## sessioninfo 1.1.1 2018-11-05 [1]
## stringi 1.4.6 2020-02-17 [1]
## stringr 1.4.0 2019-02-10 [1]
## testthat 2.3.2 2020-03-02 [1]
## tibble 3.0.1 2020-04-20 [1]
## tidyselect 1.0.0 2020-01-27 [1]
## usethis 1.6.0 2020-04-09 [1]
## vctrs 0.2.99.9010 2020-04-02 [1]
## withr 2.1.2 2018-03-15 [1]
## xfun 0.13 2020-04-13 [1]
## XVector 0.27.2 2020-03-24 [1]
## yaml 2.2.1 2020-02-01 [1]
## zlibbioc 1.33.1 2020-01-24 [1]
## source
## CRAN (R 4.0.0)
## CRAN (R 4.0.0)
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## Bioconductor
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## Github (tidyverse/dplyr@affb977)
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## Bioconductor
## Bioconductor
## Github (Bioconductor/GenomicRanges@70e6e69)
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## Bioconductor
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## Github (r-lib/rlang@a90b04b)
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## Bioconductor
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## Github (r-lib/vctrs@fd24927)
## CRAN (R 4.0.0)
## CRAN (R 4.0.0)
## Bioconductor
## CRAN (R 4.0.0)
## Bioconductor
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## [1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library