Error in if (sum(regions$qval < 0.05) < 100 & sum(regions$pval < 0.05) != : missing value where TRUE/FALSE needed #88
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Hi, we were performing an analysis for 6 samples with temporal lobe epilpepsy to look at differences in methylation @. I got this error . Error in if (sum(regions$qval < 0.05) < 100 & sum(regions$pval < 0.05) != :
missing value where TRUE/FALSE needed
I used the following settings when running the DMRichR::DM.R(
genome = c("hg38"),
testCovariate = "testCovariate",
adjustCovariate = "Age", # or NULL if no adjustment is needed
sexCheck = FALSE,
cores = 1,
coverage = 1,
perGroup = 0.1,
minCpGs = 5,
maxPerms = 6,
maxBlockPerms = 6,
cutoff = 0.05,
EnsDb = FALSE,
GOfuncR = TRUE
)
Below is the output
Smoothed (0.36 min). 1 regions scored (0 min).
...Chromosome chr9: Smoothed (0.26 min). 13 regions scored (0.12 min).
...Chromosome chr10: Smoothed (0.39 min). 3 regions scored (0.01 min).
...Chromosome chr11: Smoothed (0.37 min). 1 regions scored (0.01 min).
...Chromosome chr12: Smoothed (0.38 min). 1 regions scored (0 min).
...Chromosome chr13: Smoothed (0.24 min). 3 regions scored (0.01 min).
...Chromosome chr14: Smoothed (0.25 min). 6 regions scored (0.01 min).
...Chromosome chr15: Smoothed (0.24 min). 8 regions scored (0.02 min).
...Chromosome chr16: Smoothed (0.2 min). 2 regions scored (0 min).
...Chromosome chr17: Smoothed (0.31 min). 8 regions scored (0.01 min).
...Chromosome chr18: Smoothed (0.15 min). No candidates found.
...Chromosome chr19: Smoothed (0.21 min). 2 regions scored (0.01 min).
...Chromosome chr20: Smoothed (0.16 min). 2 regions scored (0.01 min).
...Chromosome chr21: Smoothed (0.09 min). 11 regions scored (0.26 min).
...Chromosome chr22: Smoothed (0.1 min). 5 regions scored (0.01 min).
...Chromosome chrX: Smoothed (0.33 min). 14 regions scored (0.03 min).
...Chromosome chrY: Smoothed (0.02 min). 21 regions scored (0.05 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 4
...Chromosome chr1: Smoothed (0.62 min). 18 regions scored (0.07 min).
...Chromosome chr2: Smoothed (0.62 min). 6 regions scored (0.07 min).
...Chromosome chr3: Smoothed (0.72 min). 3 regions scored (0.01 min).
...Chromosome chr4: Smoothed (0.62 min). 3 regions scored (0.02 min).
...Chromosome chr5: Smoothed (0.68 min). 6 regions scored (0.04 min).
...Chromosome chr6: Smoothed (0.61 min). 15 regions scored (0.06 min).
...Chromosome chr7: Smoothed (0.44 min). 5 regions scored (0.05 min).
...Chromosome chr8: Smoothed (0.36 min). 5 regions scored (0.03 min).
...Chromosome chr9: Smoothed (0.26 min). 5 regions scored (0.01 min).
...Chromosome chr10: Smoothed (0.39 min). 5 regions scored (0.01 min).
...Chromosome chr11: Smoothed (0.37 min). 3 regions scored (0.02 min).
...Chromosome chr12: Smoothed (0.38 min). 2 regions scored (0.01 min).
...Chromosome chr13: Smoothed (0.24 min). 5 regions scored (0.01 min).
...Chromosome chr14: Smoothed (0.26 min). 4 regions scored (0.03 min).
...Chromosome chr15: Smoothed (0.23 min). 11 regions scored (0.04 min).
...Chromosome chr16: Smoothed (0.2 min). 2 regions scored (0.01 min).
...Chromosome chr17: Smoothed (0.3 min). 10 regions scored (0.09 min).
...Chromosome chr18: Smoothed (0.15 min). 3 regions scored (0.01 min).
...Chromosome chr19: Smoothed (0.21 min). 5 regions scored (0.14 min).
...Chromosome chr20: Smoothed (0.16 min). 1 regions scored (0.04 min).
...Chromosome chr21: Smoothed (0.09 min). 7 regions scored (0.27 min).
...Chromosome chr22: Smoothed (0.1 min). No candidates found.
...Chromosome chrX: Smoothed (0.32 min). 25 regions scored (0.1 min).
...Chromosome chrY: Smoothed (0.02 min). 32 regions scored (0.21 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 5
...Chromosome chr1: Smoothed (0.63 min). 3 regions scored (0.03 min).
...Chromosome chr2: Smoothed (0.62 min). 2 regions scored (0.05 min).
...Chromosome chr3: Smoothed (0.72 min). 10 regions scored (0.06 min).
...Chromosome chr4: Smoothed (0.62 min). 3 regions scored (0.01 min).
...Chromosome chr5: Smoothed (0.68 min). 7 regions scored (0.03 min).
...Chromosome chr6: Smoothed (0.61 min). 13 regions scored (0.07 min).
...Chromosome chr7: Smoothed (0.45 min). 3 regions scored (0.02 min).
...Chromosome chr8: Smoothed (0.36 min). 4 regions scored (0.02 min).
...Chromosome chr9: Smoothed (0.26 min). 19 regions scored (0.08 min).
...Chromosome chr10: Smoothed (0.39 min). 5 regions scored (0.01 min).
...Chromosome chr11: Smoothed (0.37 min). 18 regions scored (0.09 min).
...Chromosome chr12: Smoothed (0.38 min). 2 regions scored (0.01 min).
...Chromosome chr13: Smoothed (0.24 min). 4 regions scored (0.01 min).
...Chromosome chr14: Smoothed (0.25 min). 4 regions scored (0.01 min).
...Chromosome chr15: Smoothed (0.24 min). 13 regions scored (0.02 min).
...Chromosome chr16: Smoothed (0.21 min). 2 regions scored (0.01 min).
...Chromosome chr17: Smoothed (0.31 min). 8 regions scored (0.11 min).
...Chromosome chr18: Smoothed (0.15 min). 6 regions scored (0.01 min).
...Chromosome chr19: Smoothed (0.21 min). 2 regions scored (0.03 min).
...Chromosome chr20: Smoothed (0.16 min). 12 regions scored (0.11 min).
...Chromosome chr21: Smoothed (0.09 min). 11 regions scored (0.05 min).
...Chromosome chr22: Smoothed (0.1 min). 5 regions scored (0.01 min).
...Chromosome chrX: Smoothed (0.33 min). 30 regions scored (0.12 min).
...Chromosome chrY: Smoothed (0.02 min). 29 regions scored (0.09 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 6
...Chromosome chr1: Smoothed (0.63 min). 7 regions scored (0.02 min).
...Chromosome chr2: Smoothed (0.62 min). 13 regions scored (0.2 min).
...Chromosome chr3: Smoothed (0.71 min). 2 regions scored (0.01 min).
...Chromosome chr4: Smoothed (0.63 min). 3 regions scored (0.01 min).
...Chromosome chr5: Smoothed (0.67 min). 7 regions scored (0.12 min).
...Chromosome chr6: Smoothed (0.6 min). 4 regions scored (0.02 min).
...Chromosome chr7: Smoothed (0.45 min). 2 regions scored (0 min).
...Chromosome chr8: Smoothed (0.35 min). No candidates found.
...Chromosome chr9: Smoothed (0.27 min). 3 regions scored (0.01 min).
...Chromosome chr10: Smoothed (0.45 min). 2 regions scored (0.01 min).
...Chromosome chr11: Smoothed (0.37 min). 6 regions scored (0.03 min).
...Chromosome chr12: Smoothed (0.38 min). 1 regions scored (0 min).
...Chromosome chr13: Smoothed (0.24 min). 2 regions scored (0.01 min).
...Chromosome chr14: Smoothed (0.25 min). 1 regions scored (0 min).
...Chromosome chr15: Smoothed (0.24 min). 2 regions scored (0.01 min).
...Chromosome chr16: Smoothed (0.21 min). 1 regions scored (0.01 min).
...Chromosome chr17: Smoothed (0.31 min). 13 regions scored (0.02 min).
...Chromosome chr18: Smoothed (0.15 min). 6 regions scored (0.03 min).
...Chromosome chr19: Smoothed (0.21 min). 2 regions scored (0.01 min).
...Chromosome chr20: Smoothed (0.16 min). 1 regions scored (0 min).
...Chromosome chr21: Smoothed (0.09 min). 5 regions scored (0.01 min).
...Chromosome chr22: Smoothed (0.1 min). 2 regions scored (0.01 min).
...Chromosome chrX: Smoothed (0.34 min). 16 regions scored (0.04 min).
...Chromosome chrY: Smoothed (0.02 min). 50 regions scored (0.11 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Selecting significant blocks...
Exporting block and background information...
Saving Blocks/backgroundBlocks.bed
7 significant blocks of differential methylation in 156 background blocks
Saving Blocks/blocks.bed
Annotating and plotting blocks...
[plotDMRs] Plotting DMRs
Blocks timing...
Annotating blocks with gene symbols...
Preparing HTML report...Annotating 7 regions from hg38 with gene symbols
Building CpG islands...
Building CpG shores...
Building CpG shelves...
Building inter-CpG-islands...
'select()' returned 1:many mapping between keys and columns
Done
Annotating background blocks with gene symbols...
Annotating 156 regions from hg38 with gene symbols
Building CpG islands...
Building CpG shores...
Building CpG shelves...
Building inter-CpG-islands...
'select()' returned 1:many mapping between keys and columns
Saving RData...
[DMRichR] Testing for DMRs with dmrseq 15-10-2024 06:27:22 PM
Assuming the test covariate testCovariate is a factor.
Condition: Hippocampal_Sclerosis vs Control
Adjusting for covariate (s): Age
Using a single core (backend: BiocParallel:MulticoreParam).
Computing on 1 chromosome(s) at a time.
Detecting candidate regions with coefficient larger than 0.05 in magnitude.
...Chromosome chr1: Smoothed (1.62 min). 18165 regions scored (14.06 min).
...Chromosome chr2: Smoothed (1.4 min). 15100 regions scored (11.56 min).
...Chromosome chr3: Smoothed (1.18 min). 11812 regions scored (8.68 min).
...Chromosome chr4: Smoothed (0.88 min). 11132 regions scored (8.42 min).
...Chromosome chr5: Smoothed (1.33 min). 11621 regions scored (8.72 min).
...Chromosome chr6: Smoothed (1.24 min). 9549 regions scored (7.2 min).
...Chromosome chr7: Smoothed (0.99 min). 12191 regions scored (9.5 min).
...Chromosome chr8: Smoothed (0.93 min). 9719 regions scored (7.33 min).
...Chromosome chr9: Smoothed (0.98 min). 10281 regions scored (8.29 min).
...Chromosome chr10: Smoothed (1.31 min). 10350 regions scored (8.03 min).
...Chromosome chr11: Smoothed (0.8 min). 11234 regions scored (8.88 min).
...Chromosome chr12: Smoothed (1.09 min). 9719 regions scored (7.56 min).
...Chromosome chr13: Smoothed (0.51 min). 6004 regions scored (4.6 min).
...Chromosome chr14: Smoothed (0.71 min). 6636 regions scored (5.25 min).
...Chromosome chr15: Smoothed (0.49 min). 7288 regions scored (5.71 min).
...Chromosome chr16: Smoothed (0.85 min). 9504 regions scored (8.08 min).
...Chromosome chr17: Smoothed (0.66 min). 9327 regions scored (7.99 min).
...Chromosome chr18: Smoothed (0.5 min). 6452 regions scored (4.88 min).
...Chromosome chr19: Smoothed (0.75 min). 8489 regions scored (7.48 min).
...Chromosome chr20: Smoothed (0.7 min). 6751 regions scored (5.48 min).
...Chromosome chr21: Smoothed (0.23 min). 4023 regions scored (3.3 min).
...Chromosome chr22: Smoothed (0.4 min). 6321 regions scored (5.38 min).
...Chromosome chrX: Smoothed (0.67 min). 17101 regions scored (12.56 min).
...Chromosome chrY: Smoothed (0.07 min). 2467 regions scored (1.84 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Performing balanced permutations of condition across samples to generate a null distribution of region test statistics
Beginning permutation 1
...Chromosome chr1: Smoothed (1.7 min). 103 CpG(s) excluded due to zero coverage. 19443 regions scored (15.18 min).
...Chromosome chr2: Smoothed (1.44 min). 32 CpG(s) excluded due to zero coverage. 16859 regions scored (12.78 min).
...Chromosome chr3: Smoothed (1.24 min). 38 CpG(s) excluded due to zero coverage. 13509 regions scored (9.88 min).
...Chromosome chr4: Smoothed (0.89 min). 52 CpG(s) excluded due to zero coverage. 12426 regions scored (9.2 min).
...Chromosome chr5: Smoothed (1.28 min). 117 CpG(s) excluded due to zero coverage. 13187 regions scored (9.9 min).
...Chromosome chr6: Smoothed (1.22 min). 183 CpG(s) excluded due to zero coverage. 11271 regions scored (8.31 min).
...Chromosome chr7: Smoothed (1.01 min). 49 CpG(s) excluded due to zero coverage. 13362 regions scored (10.26 min).
...Chromosome chr8: Smoothed (0.94 min). 40 CpG(s) excluded due to zero coverage. 10783 regions scored (8.14 min).
...Chromosome chr9: Smoothed (0.99 min). 81 CpG(s) excluded due to zero coverage. 11290 regions scored (9.03 min).
...Chromosome chr10: Smoothed (1.31 min). 20 CpG(s) excluded due to zero coverage. 11463 regions scored (8.89 min).
...Chromosome chr11: Smoothed (0.81 min). 38 CpG(s) excluded due to zero coverage. 12526 regions scored (9.85 min).
...Chromosome chr12: Smoothed (1.08 min). 23 CpG(s) excluded due to zero coverage. 10593 regions scored (8.11 min).
...Chromosome chr13: Smoothed (0.52 min). 14 CpG(s) excluded due to zero coverage. 6887 regions scored (5.11 min).
...Chromosome chr14: Smoothed (0.7 min). 83 CpG(s) excluded due to zero coverage. 7402 regions scored (5.84 min).
...Chromosome chr15: Smoothed (0.52 min). 177 CpG(s) excluded due to zero coverage. 7750 regions scored (6.01 min).
...Chromosome chr16: Smoothed (0.86 min). 116 CpG(s) excluded due to zero coverage. 9944 regions scored (8.36 min).
...Chromosome chr17: Smoothed (0.66 min). 269 CpG(s) excluded due to zero coverage. 9881 regions scored (8.42 min).
...Chromosome chr18: Smoothed (0.48 min). 27 CpG(s) excluded due to zero coverage. 7252 regions scored (5.35 min).
...Chromosome chr19: Smoothed (0.75 min). 54 CpG(s) excluded due to zero coverage. 8939 regions scored (8.04 min).
...Chromosome chr20: Smoothed (0.69 min). 70 CpG(s) excluded due to zero coverage. 7461 regions scored (6.37 min).
...Chromosome chr21: Smoothed (0.23 min). 82 CpG(s) excluded due to zero coverage. 4382 regions scored (3.65 min).
...Chromosome chr22: Smoothed (0.4 min). 27 CpG(s) excluded due to zero coverage. 6512 regions scored (5.57 min).
...Chromosome chrX: Smoothed (0.67 min). 132 CpG(s) excluded due to zero coverage. 18540 regions scored (13.77 min).
...Chromosome chrY: Smoothed (0.07 min). 184 CpG(s) excluded due to zero coverage. 2572 regions scored (1.86 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 2
...Chromosome chr1: Smoothed (1.66 min). 117 CpG(s) excluded due to zero coverage. 16338 regions scored (13.1 min).
...Chromosome chr2: Smoothed (1.39 min). 53 CpG(s) excluded due to zero coverage. 13091 regions scored (10.24 min).
...Chromosome chr3: Smoothed (1.18 min). 18 CpG(s) excluded due to zero coverage. 10311 regions scored (7.62 min).
...Chromosome chr4: Smoothed (0.89 min). 36 CpG(s) excluded due to zero coverage. 9452 regions scored (7.24 min).
...Chromosome chr5: Smoothed (1.31 min). 89 CpG(s) excluded due to zero coverage. 10327 regions scored (7.85 min).
...Chromosome chr6: Smoothed (1.24 min). 175 CpG(s) excluded due to zero coverage. 8473 regions scored (6.49 min).
...Chromosome chr7: Smoothed (1.02 min). 38 CpG(s) excluded due to zero coverage. 10718 regions scored (8.41 min).
...Chromosome chr8: Smoothed (0.94 min). 32 CpG(s) excluded due to zero coverage. 8384 regions scored (6.54 min).
...Chromosome chr9: Smoothed (0.99 min). 36 CpG(s) excluded due to zero coverage. 9221 regions scored (7.53 min).
...Chromosome chr10: Smoothed (1.31 min). 32 CpG(s) excluded due to zero coverage. 9341 regions scored (7.35 min).
...Chromosome chr11: Smoothed (0.8 min). 59 CpG(s) excluded due to zero coverage. 10549 regions scored (8.48 min).
...Chromosome chr12: Smoothed (1.07 min). 25 CpG(s) excluded due to zero coverage. 8174 regions scored (6.43 min).
...Chromosome chr13: Smoothed (0.52 min). 29 CpG(s) excluded due to zero coverage. 5155 regions scored (4.05 min).
...Chromosome chr14: Smoothed (0.71 min). 77 CpG(s) excluded due to zero coverage. 6016 regions scored (4.8 min).
...Chromosome chr15: Smoothed (0.5 min). 105 CpG(s) excluded due to zero coverage. 6581 regions scored (5.24 min).
...Chromosome chr16: Smoothed (0.87 min). 121 CpG(s) excluded due to zero coverage. 8692 regions scored (7.48 min).
...Chromosome chr17: Smoothed (0.67 min). 240 CpG(s) excluded due to zero coverage. 8557 regions scored (7.46 min).
...Chromosome chr18: Smoothed (0.49 min). 10 CpG(s) excluded due to zero coverage. 5940 regions scored (4.49 min).
...Chromosome chr19: Smoothed (0.76 min). 34 CpG(s) excluded due to zero coverage. 7996 regions scored (7.13 min).
...Chromosome chr20: Smoothed (0.7 min). 45 CpG(s) excluded due to zero coverage. 6276 regions scored (5.23 min).
...Chromosome chr21: Smoothed (0.23 min). 91 CpG(s) excluded due to zero coverage. 3674 regions scored (3.17 min).
...Chromosome chr22: Smoothed (0.39 min). 32 CpG(s) excluded due to zero coverage. 6051 regions scored (5.32 min).
...Chromosome chrX: Smoothed (0.67 min). 87 CpG(s) excluded due to zero coverage. 15889 regions scored (12.01 min).
...Chromosome chrY: Smoothed (0.07 min). 200 CpG(s) excluded due to zero coverage. 2239 regions scored (1.69 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 3
...Chromosome chr1: Smoothed (1.72 min). 83 CpG(s) excluded due to zero coverage. 17409 regions scored (13.93 min).
...Chromosome chr2: Smoothed (1.4 min). 39 CpG(s) excluded due to zero coverage. 14153 regions scored (10.98 min).
...Chromosome chr3: Smoothed (1.17 min). 39 CpG(s) excluded due to zero coverage. 11263 regions scored (8.47 min).
...Chromosome chr4: Smoothed (0.88 min). 44 CpG(s) excluded due to zero coverage. 10106 regions scored (7.72 min).
...Chromosome chr5: Smoothed (1.3 min). 73 CpG(s) excluded due to zero coverage. 11108 regions scored (8.4 min).
...Chromosome chr6: Smoothed (1.24 min). 246 CpG(s) excluded due to zero coverage. 9179 regions scored (6.98 min).
...Chromosome chr7: Smoothed (1.01 min). 59 CpG(s) excluded due to zero coverage. 11696 regions scored (9.12 min).
...Chromosome chr8: Smoothed (0.95 min). 29 CpG(s) excluded due to zero coverage. 9180 regions scored (7.15 min).
...Chromosome chr9: Smoothed (0.99 min). 44 CpG(s) excluded due to zero coverage. 9913 regions scored (8.15 min).
...Chromosome chr10: Smoothed (1.32 min). 15 CpG(s) excluded due to zero coverage. 9967 regions scored (7.88 min).
...Chromosome chr11: Smoothed (0.81 min). 51 CpG(s) excluded due to zero coverage. 10959 regions scored (8.83 min).
...Chromosome chr12: Smoothed (1.09 min). 28 CpG(s) excluded due to zero coverage. 8944 regions scored (6.85 min).
...Chromosome chr13: Smoothed (0.53 min). 17 CpG(s) excluded due to zero coverage. 5603 regions scored (4.31 min).
...Chromosome chr14: Smoothed (0.73 min). 104 CpG(s) excluded due to zero coverage. 6376 regions scored (5.14 min).
...Chromosome chr15: Smoothed (0.51 min). 164 CpG(s) excluded due to zero coverage. 6954 regions scored (5.52 min).
...Chromosome chr16: Smoothed (0.86 min). 62 CpG(s) excluded due to zero coverage. 9291 regions scored (7.95 min).
...Chromosome chr17: Smoothed (0.66 min). 200 CpG(s) excluded due to zero coverage. 8870 regions scored (7.53 min).
...Chromosome chr18: Smoothed (0.49 min). 27 CpG(s) excluded due to zero coverage. 6337 regions scored (4.75 min).
...Chromosome chr19: Smoothed (0.76 min). 25 CpG(s) excluded due to zero coverage. 8295 regions scored (7.32 min).
...Chromosome chr20: Smoothed (0.7 min). 4 CpG(s) excluded due to zero coverage. 6501 regions scored (5.29 min).
...Chromosome chr21: Smoothed (0.23 min). 64 CpG(s) excluded due to zero coverage. 3863 regions scored (3.35 min).
...Chromosome chr22: Smoothed (0.4 min). 42 CpG(s) excluded due to zero coverage. 6202 regions scored (5.47 min).
...Chromosome chrX: Smoothed (0.68 min). 157 CpG(s) excluded due to zero coverage. 16596 regions scored (12.48 min).
...Chromosome chrY: Smoothed (0.07 min). 158 CpG(s) excluded due to zero coverage. 2519 regions scored (1.83 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 4
...Chromosome chr1: Smoothed (1.68 min). 103 CpG(s) excluded due to zero coverage. 16546 regions scored (13.42 min).
...Chromosome chr2: Smoothed (1.4 min). 49 CpG(s) excluded due to zero coverage. 13590 regions scored (10.73 min).
...Chromosome chr3: Smoothed (1.17 min). 16 CpG(s) excluded due to zero coverage. 10757 regions scored (8.05 min).
...Chromosome chr4: Smoothed (0.9 min). 39 CpG(s) excluded due to zero coverage. 9585 regions scored (7.42 min).
...Chromosome chr5: Smoothed (1.28 min). 90 CpG(s) excluded due to zero coverage. 10595 regions scored (8.15 min).
...Chromosome chr6: Smoothed (1.24 min). 221 CpG(s) excluded due to zero coverage. 8871 regions scored (6.89 min).
...Chromosome chr7: Smoothed (1.02 min). 59 CpG(s) excluded due to zero coverage. 11176 regions scored (8.75 min).
...Chromosome chr8: Smoothed (0.95 min). 81 CpG(s) excluded due to zero coverage. 8692 regions scored (6.74 min).
...Chromosome chr9: Smoothed (0.99 min). 42 CpG(s) excluded due to zero coverage. 9755 regions scored (8.04 min).
...Chromosome chr10: Smoothed (1.32 min). 23 CpG(s) excluded due to zero coverage. 9482 regions scored (7.46 min).
...Chromosome chr11: Smoothed (0.81 min). 22 CpG(s) excluded due to zero coverage. 10494 regions scored (8.52 min).
...Chromosome chr12: Smoothed (1.08 min). 10 CpG(s) excluded due to zero coverage. 8771 regions scored (6.75 min).
...Chromosome chr13: Smoothed (0.53 min). 19 CpG(s) excluded due to zero coverage. 5267 regions scored (4.13 min).
...Chromosome chr14: Smoothed (0.72 min). 97 CpG(s) excluded due to zero coverage. 6118 regions scored (4.97 min).
...Chromosome chr15: Smoothed (0.5 min). 151 CpG(s) excluded due to zero coverage. 6861 regions scored (5.42 min).
...Chromosome chr16: Smoothed (0.86 min). 98 CpG(s) excluded due to zero coverage. 8933 regions scored (7.62 min).
...Chromosome chr17: Smoothed (0.67 min). 198 CpG(s) excluded due to zero coverage. 8881 regions scored (7.71 min).
...Chromosome chr18: Smoothed (0.48 min). 28 CpG(s) excluded due to zero coverage. 6136 regions scored (4.6 min).
...Chromosome chr19: Smoothed (0.74 min). 20 CpG(s) excluded due to zero coverage. 8153 regions scored (7.23 min).
...Chromosome chr20: Smoothed (0.72 min). 1 CpG(s) excluded due to zero coverage. 6340 regions scored (5.23 min).
...Chromosome chr21: Smoothed (0.23 min). 54 CpG(s) excluded due to zero coverage. 3783 regions scored (3.35 min).
...Chromosome chr22: Smoothed (0.4 min). 62 CpG(s) excluded due to zero coverage. 6148 regions scored (5.46 min).
...Chromosome chrX: Smoothed (0.69 min). 151 CpG(s) excluded due to zero coverage. 16075 regions scored (12.17 min).
...Chromosome chrY: Smoothed (0.08 min). 173 CpG(s) excluded due to zero coverage. 2411 regions scored (1.8 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 5
...Chromosome chr1: Smoothed (1.72 min). 116 CpG(s) excluded due to zero coverage. 16556 regions scored (13.45 min).
...Chromosome chr2: Smoothed (1.41 min). 24 CpG(s) excluded due to zero coverage. 13158 regions scored (10.38 min).
...Chromosome chr3: Smoothed (1.17 min). 31 CpG(s) excluded due to zero coverage. 10343 regions scored (7.82 min).
...Chromosome chr4: Smoothed (0.9 min). 40 CpG(s) excluded due to zero coverage. 9351 regions scored (7.26 min).
...Chromosome chr5: Smoothed (1.31 min). 125 CpG(s) excluded due to zero coverage. 10112 regions scored (7.92 min).
...Chromosome chr6: Smoothed (1.27 min). 211 CpG(s) excluded due to zero coverage. 8612 regions scored (6.73 min).
...Chromosome chr7: Smoothed (1.02 min). 38 CpG(s) excluded due to zero coverage. 10998 regions scored (8.69 min).
...Chromosome chr8: Smoothed (0.94 min). 49 CpG(s) excluded due to zero coverage. 8479 regions scored (6.69 min).
...Chromosome chr9: Smoothed (1 min). 86 CpG(s) excluded due to zero coverage. 9452 regions scored (7.83 min).
...Chromosome chr10: Smoothed (1.33 min). 74 CpG(s) excluded due to zero coverage. 9289 regions scored (7.42 min).
...Chromosome chr11: Smoothed (0.82 min). 56 CpG(s) excluded due to zero coverage. 10466 regions scored (8.4 min).
...Chromosome chr12: Smoothed (1.1 min). 22 CpG(s) excluded due to zero coverage. 8495 regions scored (6.7 min).
...Chromosome chr13: Smoothed (0.53 min). 27 CpG(s) excluded due to zero coverage. 5192 regions scored (4.04 min).
...Chromosome chr14: Smoothed (0.72 min). 49 CpG(s) excluded due to zero coverage. 5997 regions scored (4.78 min).
...Chromosome chr15: Smoothed (0.5 min). 150 CpG(s) excluded due to zero coverage. 6595 regions scored (5.33 min).
...Chromosome chr16: Smoothed (0.86 min). 56 CpG(s) excluded due to zero coverage. 8837 regions scored (7.54 min).
...Chromosome chr17: Smoothed (0.65 min). 331 CpG(s) excluded due to zero coverage. 8670 regions scored (7.54 min).
...Chromosome chr18: Smoothed (0.48 min). 10 CpG(s) excluded due to zero coverage. 5966 regions scored (4.55 min).
...Chromosome chr19: Smoothed (0.75 min). 36 CpG(s) excluded due to zero coverage. 8063 regions scored (7.14 min).
...Chromosome chr20: Smoothed (0.7 min). 62 CpG(s) excluded due to zero coverage. 6211 regions scored (5.18 min).
...Chromosome chr21: Smoothed (0.24 min). 73 CpG(s) excluded due to zero coverage. 3746 regions scored (3.35 min).
...Chromosome chr22: Smoothed (0.4 min). 25 CpG(s) excluded due to zero coverage. 6091 regions scored (5.16 min).
...Chromosome chrX: Smoothed (0.67 min). 91 CpG(s) excluded due to zero coverage. 15826 regions scored (12.02 min).
...Chromosome chrY: Smoothed (0.08 min). 206 CpG(s) excluded due to zero coverage. 2370 regions scored (1.75 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Beginning permutation 6
...Chromosome chr1: Smoothed (1.64 min). 168 CpG(s) excluded due to zero coverage. 16928 regions scored (13.77 min).
...Chromosome chr2: Smoothed (1.41 min). 23 CpG(s) excluded due to zero coverage. 13266 regions scored (10.43 min).
...Chromosome chr3: Smoothed (1.22 min). 48 CpG(s) excluded due to zero coverage. 10999 regions scored (8.23 min).
...Chromosome chr4: Smoothed (0.89 min). 49 CpG(s) excluded due to zero coverage. 10040 regions scored (7.67 min).
...Chromosome chr5: Smoothed (1.3 min). 81 CpG(s) excluded due to zero coverage. 10759 regions scored (8.32 min).
...Chromosome chr6: Smoothed (1.27 min). 155 CpG(s) excluded due to zero coverage. 9213 regions scored (7.04 min).
...Chromosome chr7: Smoothed (1.02 min). 79 CpG(s) excluded due to zero coverage. 11210 regions scored (8.84 min).
...Chromosome chr8: Smoothed (0.96 min). 90 CpG(s) excluded due to zero coverage. 8700 regions scored (6.75 min).
...Chromosome chr9: Smoothed (1 min). 83 CpG(s) excluded due to zero coverage. 9642 regions scored (8.02 min).
...Chromosome chr10: Smoothed (1.32 min). 71 CpG(s) excluded due to zero coverage. 9750 regions scored (7.68 min).
...Chromosome chr11: Smoothed (0.83 min). 34 CpG(s) excluded due to zero coverage. 10865 regions scored (9.34 min).
...Chromosome chr12: Smoothed (1.1 min). 21 CpG(s) excluded due to zero coverage. 8644 regions scored (6.74 min).
...Chromosome chr13: Smoothed (0.53 min). 8 CpG(s) excluded due to zero coverage. 5361 regions scored (4.2 min).
...Chromosome chr14: Smoothed (0.71 min). 65 CpG(s) excluded due to zero coverage. 6189 regions scored (4.95 min).
...Chromosome chr15: Smoothed (0.51 min). 160 CpG(s) excluded due to zero coverage. 6790 regions scored (5.43 min).
...Chromosome chr16: Smoothed (0.86 min). 85 CpG(s) excluded due to zero coverage. 8909 regions scored (7.75 min).
...Chromosome chr17: Smoothed (0.66 min). 277 CpG(s) excluded due to zero coverage. 8866 regions scored (7.55 min).
...Chromosome chr18: Smoothed (0.49 min). 7 CpG(s) excluded due to zero coverage. 6158 regions scored (4.61 min).
...Chromosome chr19: Smoothed (0.76 min). 22 CpG(s) excluded due to zero coverage. 8026 regions scored (7.1 min).
...Chromosome chr20: Smoothed (0.71 min). 52 CpG(s) excluded due to zero coverage. 6401 regions scored (5.19 min).
...Chromosome chr21: Smoothed (0.23 min). 47 CpG(s) excluded due to zero coverage. 3835 regions scored (3.23 min).
...Chromosome chr22: Smoothed (0.4 min). 16 CpG(s) excluded due to zero coverage. 6170 regions scored (5.31 min).
...Chromosome chrX: Smoothed (0.68 min). 138 CpG(s) excluded due to zero coverage. 16556 regions scored (12.31 min).
...Chromosome chrY: Smoothed (0.07 min). 288 CpG(s) excluded due to zero coverage. 2489 regions scored (1.86 min).
...Chromosome chrM: Smoothed (0 min). No candidates found.
Selecting significant DMRs...
Error in if (sum(regions$qval < 0.05) < 100 & sum(regions$pval < 0.05) != :
missing value where TRUE/FALSE needed
In addition: There were 50 or more warnings (use warnings() to see the first 50)
The text was updated successfully, but these errors were encountered: