Last updated: 2021-09-24
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Knit directory: femNATCD_MethSeq/
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## load Data ####
load(paste0(Home,"/output/dds_filt_analyzed.RData"))ranges=as.data.frame(rowRanges(dds_filt))
log_cpm = log2(counts(dds_filt, normalized=T)+1)
BootN = 250
GapSize = 500
if (reanalyze){
cl <- clusterMaker(ranges$seqnames, ranges$start, maxGap = GapSize)
tab=table(cl)
designmatrix = model.matrix(design(dds_filt), colData(dds_filt))
resdmr = bumphunter(log_cpm,
design=designmatrix,
pos=ranges$start,
chr=ranges$seqnames,
coef=ncol(designmatrix), cluster=cl, cutoff=0.5, nullMethod = "bootstrap", B=BootN)
bumphunter:::foreachCleanup()
save(resdmr, file=paste0(Home,"/output/resdmr.RData"))
} else {
if(file.exists(paste0(Home,"/output/resdmr.RData"))){
load(paste0(Home,"/output/resdmr.RData"))
} else {
cl <- clusterMaker(ranges$seqnames, ranges$start, maxGap = GapSize)
tab=table(cl)
designmatrix = model.matrix(design(dds_filt), colData(dds_filt))
resdmr = bumphunter(log_cpm,
design=designmatrix,
pos=ranges$start,
chr=ranges$seqnames,
coef=ncol(designmatrix), cluster=cl, cutoff=0.5, nullMethod = "bootstrap", B=BootN)
}
}
subject = annotateTranscripts(txdb = TxDb.Hsapiens.UCSC.hg19.knownGene,
by="gene")No annotationPackage supplied. Trying org.Hs.eg.db.Lade nötiges Paket: org.Hs.eg.dbGetting TSS and TSE. 403 genes were dropped because they have exons located on both strands
of the same reference sequence or on more than one reference sequence,
so cannot be represented by a single genomic range.
Use 'single.strand.genes.only=FALSE' to get all the genes in a
GRangesList object, or use suppressMessages() to suppress this message.Getting CSS and CSE.Getting exons.Annotating genes.resultsdmr_table = resdmr$table
subject = subject[subject@seqnames %in% unique(resultsdmr_table$chr),]
chck = matchGenes(resultsdmr_table, subject, type ="any", promoterDist = 2000).................................................................................resultsdmr_table = cbind(resultsdmr_table, chck)
display_tab_simple(head(resultsdmr_table, n=10))| chr | start | end | value | area | cluster | indexStart | indexEnd | L | clusterL | p.value | fwer | p.valueArea | fwerArea | name | annotation | description | region | distance | subregion | insideDistance | exonnumber | nexons | UTR | strand | geneL | codingL | Geneid | subjectHits | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 3194 | chr3 | 24561792 | 24561792 | -1.365 | 1.365 | 16970 | 35466 | 35466 | 1 | 1 | 0.000 | 0.268 | 0.004 | 0.980 | NA | NA | close to 3’ | close to 3’ | 1134 | NA | NA | NA | 1 | NA |
|
73 | NA | 100616448 | 1791 |
| 6414 | chr16 | 87636490 | 87636843 | -0.647 | 1.941 | 75725 | 158341 | 158343 | 3 | 10 | 0.000 | 0.420 | 0.000 | 0.464 | JPH3 | NM_001271604 NM_001271605 NM_020655 NP_001258533 NP_001258534 NP_065706 NR_073379 | overlaps exon upstream | inside | 1049 | overlaps exon upstream | 0 | 2 | 7 | overlaps 5’ UTR |
|
96320 | NA | 57338 | 15750 |
| 6516 | chr17 | 5403095 | 5403469 | -0.640 | 1.919 | 76781 | 160823 | 160825 | 3 | 8 | 0.000 | 0.444 | 0.000 | 0.488 | LOC728392 | NM_001162371 NP_001155843 | overlaps two exons | inside | 850 | overlaps two exons | 0 | 2 | 2 | 3’UTR |
|
1572 | NA | 728392 | 18663 |
| 5076 | chr10 | 135088739 | 135088739 | -1.289 | 1.289 | 52539 | 109119 | 109119 | 1 | 14 | 0.000 | 0.472 | 0.006 | 0.996 | ADAM8 | NM_001109 NM_001164489 NM_001164490 NP_001100 NP_001157961 NP_001157962 XM_011539117 XM_017015465 XM_017015466 XP_011537419 XP_016870954 XP_016870955 | inside intron | inside | 1668 | inside intron | 248 | 3 | 23 | inside transcription region |
|
14487 | NA | 101 | 2152 |
| 2559 | chr1 | 68151243 | 68151858 | -0.537 | 1.610 | 4738 | 10048 | 10050 | 3 | 11 | 0.000 | 0.756 | 0.001 | 0.856 | GADD45A | NM_001199741 NM_001199742 NM_001924 NP_001186670 NP_001186671 NP_001915 | covers exon(s) | inside | 383 | covers exon(s) | 0 | 1 | 4 | inside transcription region |
|
3161 | NA | 1647 | 5589 |
| 3396 | chr3 | 195943548 | 195943548 | -1.192 | 1.192 | 21455 | 44421 | 44421 | 1 | 5 | 0.001 | 0.808 | 0.010 | 1.000 | SLC51A | NM_152672 NP_689885 | inside exon | inside | 165 | inside exon | 0 | 1 | 8 | 5’ UTR |
|
16918 | NA | 200931 | 6115 |
| 5489 | chr12 | 50348045 | 50348422 | -0.778 | 1.555 | 60025 | 125369 | 125370 | 2 | 5 | 0.001 | 0.812 | 0.001 | 0.896 | AQP2 | NM_000486 NP_000477 | overlaps two exons | inside | 3521 | overlaps two exons | 0 | 2 | 4 | inside transcription region |
|
8140 | NA | 359 | 10625 |
| 7597 | chr21 | 34696824 | 34696854 | -0.776 | 1.552 | 93519 | 199373 | 199374 | 2 | 5 | 0.001 | 0.812 | 0.001 | 0.896 | IFNAR1 | NM_000629 NM_001384498 NM_001384499 NM_001384500 NM_001384501 NM_001384502 NM_001384503 NM_001384504 NP_000620 NP_001371427 NP_001371428 NP_001371429 NP_001371430 NP_001371431 NP_001371432 NP_001371433 XM_011529552 XP_011527854 | inside exon | inside | 90 | inside exon | 0 | 1 | 12 | 5’ UTR |
|
35394 | NA | 3454 | 10411 |
| 5983 | chr15 | 31652488 | 31652665 | -0.768 | 1.536 | 68659 | 143276 | 143277 | 2 | 7 | 0.001 | 0.824 | 0.001 | 0.904 | KLF13 | NM_001302461 NM_015995 NP_001289390 NP_057079 NR_033741 | inside intron | inside | 33405 | inside intron | 11547 | 2 | 2 | inside transcription region |
|
51019 | NA | 51621 | 13653 |
| 5730 | chr13 | 88324376 | 88324376 | -1.187 | 1.187 | 64598 | 134778 | 134778 | 1 | 10 | 0.001 | 0.828 | 0.010 | 1.000 | SLITRK5 | NM_001384609 NM_001384610 NM_015567 NP_001371538 NP_001371539 NP_056382 | promoter | promoter | 494 | NA | NA | NA | 2 | NA |
|
7000 | NA | 26050 | 8052 |
Nsig_region = sum(resultsdmr_table$fwer<=0.2)
Sighits = resultsdmr_table[resultsdmr_table$fwer<=0.2,]
save(resultsdmr_table, file=paste0(Home,"/output/resultsdmr_table.RData"))
save(resdmr, file=paste0(Home,"/output/resdmr.RData"))
res_dmr_filtered = resultsdmr_table %>% dplyr::select(-annotation)
write.csv(resultsdmr_table, file = paste0(Home,"/output/DMR_Results.csv"), row.names = T)
sessionInfo()R version 4.0.3 (2020-10-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
[5] LC_TIME=German_Germany.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] org.Hs.eg.db_3.12.0
[2] scales_1.1.1
[3] RCircos_1.2.1
[4] compareGroups_4.4.6
[5] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[6] GenomicFeatures_1.42.1
[7] AnnotationDbi_1.52.0
[8] bumphunter_1.32.0
[9] locfit_1.5-9.4
[10] doParallel_1.0.16
[11] iterators_1.0.13
[12] foreach_1.5.1
[13] kableExtra_1.3.1
[14] forcats_0.5.0
[15] stringr_1.4.0
[16] dplyr_1.0.2
[17] purrr_0.3.4
[18] readr_1.4.0
[19] tidyr_1.1.2
[20] tibble_3.0.4
[21] ggplot2_3.3.3
[22] tidyverse_1.3.0
[23] DESeq2_1.30.0
[24] SummarizedExperiment_1.20.0
[25] Biobase_2.50.0
[26] MatrixGenerics_1.2.0
[27] matrixStats_0.57.0
[28] GenomicRanges_1.42.0
[29] GenomeInfoDb_1.26.2
[30] IRanges_2.24.1
[31] S4Vectors_0.28.1
[32] BiocGenerics_0.36.0
[33] RColorBrewer_1.1-2
[34] knitr_1.30
[35] workflowr_1.6.2
loaded via a namespace (and not attached):
[1] readxl_1.3.1 uuid_0.1-4 backports_1.2.0
[4] systemfonts_0.3.2 BiocFileCache_1.14.0 splines_4.0.3
[7] BiocParallel_1.24.1 digest_0.6.27 htmltools_0.5.1.1
[10] fansi_0.4.1 magrittr_2.0.1 Rsolnp_1.16
[13] memoise_2.0.0 Biostrings_2.58.0 annotate_1.68.0
[16] modelr_0.1.8 officer_0.3.16 askpass_1.1
[19] prettyunits_1.1.1 colorspace_2.0-0 blob_1.2.1
[22] rvest_0.3.6 rappdirs_0.3.1 haven_2.3.1
[25] xfun_0.20 crayon_1.3.4 RCurl_1.98-1.2
[28] jsonlite_1.7.2 genefilter_1.72.0 survival_3.2-7
[31] glue_1.4.2 gtable_0.3.0 zlibbioc_1.36.0
[34] XVector_0.30.0 webshot_0.5.2 DelayedArray_0.16.0
[37] DBI_1.1.1 rngtools_1.5 Rcpp_1.0.5
[40] viridisLite_0.3.0 xtable_1.8-4 progress_1.2.2
[43] bit_4.0.4 truncnorm_1.0-8 httr_1.4.2
[46] ellipsis_0.3.1 mice_3.12.0 pkgconfig_2.0.3
[49] XML_3.99-0.5 dbplyr_2.0.0 tidyselect_1.1.0
[52] rlang_0.4.10 later_1.1.0.1 munsell_0.5.0
[55] cellranger_1.1.0 tools_4.0.3 cachem_1.0.1
[58] cli_2.2.0 generics_0.1.0 RSQLite_2.2.2
[61] broom_0.7.3 evaluate_0.14 fastmap_1.1.0
[64] yaml_2.2.1 bit64_4.0.5 fs_1.5.0
[67] zip_2.1.1 doRNG_1.8.2 whisker_0.4
[70] xml2_1.3.2 biomaRt_2.46.2 compiler_4.0.3
[73] rstudioapi_0.13 curl_4.3 reprex_1.0.0
[76] geneplotter_1.68.0 stringi_1.5.3 HardyWeinberg_1.7.1
[79] highr_0.8 ps_1.5.0 gdtools_0.2.3
[82] lattice_0.20-41 Matrix_1.2-18 vctrs_0.3.6
[85] pillar_1.4.7 lifecycle_0.2.0 data.table_1.13.6
[88] bitops_1.0-6 flextable_0.6.2 httpuv_1.5.5
[91] rtracklayer_1.49.5 R6_2.5.0 promises_1.1.1
[94] writexl_1.3.1 codetools_0.2-18 assertthat_0.2.1
[97] chron_2.3-56 openssl_1.4.3 rprojroot_2.0.2
[100] withr_2.4.1 GenomicAlignments_1.26.0 Rsamtools_2.6.0
[103] GenomeInfoDbData_1.2.4 hms_1.0.0 grid_4.0.3
[106] rmarkdown_2.6 git2r_0.28.0 base64enc_0.1-3
[109] lubridate_1.7.9.2