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Thanks so much pointing me to this, Christian.I have installed the package and have it running. I have p-values for all the CpGs.Does it matter than when I run the makeCpGregions step, I am reading in p-values rather than t-values? I don't see a way to specify this in the manual and when I look at the resulting GRangesList object, I see the p-values are listed as t-values (below).Also, it seems like the GRangesList object only contains clusters on chr 1, even though I have CpGs on all autosomes.Thank you for your help with this!Elaine#command to cluster CpGs#observations is a vector of p-values, chr a vector of chromosomes, and coord a vector of start coordinates.regions <- makeCpGregions(observations = observations, chr = chr, pos = coord, maxGap = 1000, minCpG = 3)head(regions)GRangesList object of length 355:[[1]]GRanges object with 22 ranges and 3 metadata columns:seqnames ranges strand | no.cpgs tVal id<Rle> <IRanges> <Rle> | <integer> <numeric> <character>[1] 1 877647 * | 22 5.51491355618062e-11 cg19724344[2] 1 877489 * | 22 6.53804673624079e-09 cg09988062[3] 1 860022 * | 22 7.8374456386125e-09 cg25215298[4] 1 843491 * | 22 1.35019341172262e-08 cg01097950[5] 1 860965 * | 22 3.49094251377986e-08 cg03180780
On Fri, May 10, 2019 at 4:38 AM Christian Page <christ...@medisin.uio.no> wrote:
Hi Elaine,--There is an R-package called DMRScan (https://bioconductor.org/packages/release/bioc/html/DMRScan.html) in Bioconductor that can create DMRs from the p-value/test-statistic for a set of CpG sites. It uses all CpG sites and not only the significant ones to create the DMRs, so you might need to retain the p-values for the full set of CpGs.Best,Christian
On Wednesday, April 17, 2019 at 12:10:50 AM UTC+2, elainee...@gmail.com wrote:Hi all,I have identified differentially methylated positions from illumina EPIC methylation array data using a linear mixed model. Because I have related individuals in my sample, I needed to account for relatedness using a kinship matrix as a random effect. I would like to identify DMRs from the list of DMPs I have identified with my mixed model. But none of the approaches I have seen for identifying DMRs seem compatible with this.Does anyone know of a function (preferably implemented in R) for identifying DMRs from a custom list of DMPs?Thank you!Elaine
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