I like to run QTL analysis using Matrixeqtl on the normalized beta values from my epic array to the genotypes of the same samples.
The issue is epic array data run ( Minfi & DMRcate )is based on IlluminaHumanMethylationEPICanno.ilm10b4.hg19 and the Genotype is based on Grch38.
How could I liftover the Position of CpgIDs from hg19 to grch38 to run QTL analysis(matrixQTL needs gene(cpg) cordinates)
Do you think ensembl lifover "https://asia.ensembl.org/Homo_sapiens/Tools/AssemblyConverter?db=core" and using the bed file formate a way?
`sessionInfo()`
> R version 3.5.1 (2018-07-02)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)
Matrix products: default
BLAS/LAPACK: /scratch/mv83/Software/DMRcate/lib/R/lib/libRblas.so
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats4 parallel stats graphics grDevices utils
[8] datasets methods base
other attached packages:
[1] IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0
[2] DMRcate_1.18.0
[3] DMRcatedata_1.16.0
[4] DSS_2.30.0
[5] bsseq_1.18.0
[6] minfi_1.28.0
[7] bumphunter_1.24.5
[8] locfit_1.5-9.1
[9] iterators_1.0.10
[10] foreach_1.4.4
[11] Biostrings_2.50.2
[12] XVector_0.22.0
[13] SummarizedExperiment_1.12.0
[14] DelayedArray_0.8.0
[15] BiocParallel_1.16.2
[16] matrixStats_0.54.0
[17] Biobase_2.42.0
[18] GenomicRanges_1.34.0
[19] GenomeInfoDb_1.18.1
[20] IRanges_2.16.0
[21] S4Vectors_0.20.1
[22] BiocGenerics_0.28.0
loaded via a namespace (and not attached):
[1] backports_1.1.3
[2] Hmisc_4.1-1
[3] plyr_1.8.4
[4] lazyeval_0.2.2
[5] ggplot2_3.1.1
[6] digest_0.6.18
[7] ensembldb_2.6.3
[8] htmltools_0.3.6
[9] GO.db_3.7.0
[10] magrittr_1.5
[11] checkmate_1.9.1
[12] memoise_1.1.0
[13] BSgenome_1.50.0
[14] cluster_2.0.8
[15] limma_3.36.5
[16] readr_1.3.1
[17] annotate_1.60.0
[18] R.utils_2.8.0
[19] askpass_1.1
[20] siggenes_1.56.0
[21] prettyunits_1.0.2
[22] colorspace_1.4-1
[23] blob_1.1.1
[24] BiasedUrn_1.07
[25] xfun_0.6
[26] dplyr_0.8.0.1
[27] crayon_1.3.4
[28] RCurl_1.95-4.12
[29] genefilter_1.64.0
[30] GEOquery_2.50.0
[31] IlluminaHumanMethylationEPICmanifest_0.3.0
[32] survival_2.44-1.1
[33] VariantAnnotation_1.28.3
[34] glue_1.3.1
[35] ruv_0.9.6
[36] registry_0.5
[37] gtable_0.3.0
[38] zlibbioc_1.28.0
[39] Rhdf5lib_1.4.3
[40] HDF5Array_1.10.1
[41] scales_1.0.0
[42] DBI_1.0.0
[43] rngtools_1.3.1
[44] bibtex_0.4.2
[45] Rcpp_1.0.1
[46] xtable_1.8-3
[47] progress_1.2.0
[48] htmlTable_1.13.1
[49] foreign_0.8-71
[50] bit_1.1-14
[51] mclust_5.4.3
[52] preprocessCore_1.44.0
[53] Formula_1.2-3
[54] missMethyl_1.16.0
[55] htmlwidgets_1.3
[56] httr_1.4.0
[57] RColorBrewer_1.1-2
[58] acepack_1.4.1
[59] pkgconfig_2.0.2
[60] reshape_0.8.8
[61] XML_3.98-1.16
[62] R.methodsS3_1.7.1
[63] Gviz_1.26.4
[64] nnet_7.3-12
[65] tidyselect_0.2.5
[66] rlang_0.3.3
[67] AnnotationDbi_1.44.0
[68] munsell_0.5.0
[69] tools_3.5.1
[70] RSQLite_2.1.1
[71] stringr_1.4.0
[72] org.Hs.eg.db_3.7.0
[73] knitr_1.22
[74] bit64_0.9-7
[75] beanplot_1.2
[76] methylumi_2.28.0
[77] purrr_0.3.2
[78] AnnotationFilter_1.6.0
[79] nlme_3.1-137
[80] doRNG_1.7.1
[81] nor1mix_1.2-3
[82] R.oo_1.22.0
[83] xml2_1.2.0
[84] biomaRt_2.38.0
[85] compiler_3.5.1
[86] rstudioapi_0.10
[87] curl_3.3
[88] statmod_1.4.30
[89] tibble_2.1.1
[90] stringi_1.4.3
[91] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0
[92] GenomicFeatures_1.34.1
[93] lattice_0.20-38
[94] ProtGenerics_1.14.0
[95] Matrix_1.2-17
[96] IlluminaHumanMethylation450kmanifest_0.4.0
[97] permute_0.9-5
[98] multtest_2.38.0
[99] pillar_1.3.1
[100] data.table_1.12.2
[101] bitops_1.0-6
[102] rtracklayer_1.42.1
[103] R6_2.4.0
[104] latticeExtra_0.6-28
[105] gridExtra_2.3
[106] codetools_0.2-16
[107] dichromat_2.0-0
[108] MASS_7.3-51.3
[109] gtools_3.8.1
[110] assertthat_0.2.1
[111] rhdf5_2.26.2
[112] openssl_1.3
[113] pkgmaker_0.27
[114] withr_2.1.2
[115] GenomicAlignments_1.18.1
[116] Rsamtools_1.34.0
[117] GenomeInfoDbData_1.1.0
[118] hms_0.4.2
[119] quadprog_1.5-5
[120] grid_3.5.1
[121] rpart_4.1-13
[122] tidyr_0.8.3
[123] base64_2.0
[124] DelayedMatrixStats_1.4.0
[125] illuminaio_0.24.0
[126] biovizBase_1.30.1
[127] base64enc_0.1-3`
Thanks this works for me
Thanks this works for me