R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core) Matrix products: default BLAS/LAPACK: /gscratch/sw/intel-2019/compilers_and_libraries_2019.0.117/linux/mkl/lib/intel64_lin/libmkl_rt.so locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] compiler_3.6.0 Attaching package: ‘dplyr’ The following objects are masked from ‘package:data.table’: between, first, last The following objects are masked from ‘package:stats’: filter, lag The following objects are masked from ‘package:base’: intersect, setdiff, setequal, union 'data.frame': 11537615 obs. of 17 variables: $ loci : chr "scaffold1_cov55:102-104" "scaffold1_cov55:105-107" "scaffold1_cov55:116-118" "scaffold1_cov55:119-121" ... $ method : chr "WGBS" "WGBS" "WGBS" "WGBS" ... $ medn_meth : num 0 0 0 0 0 0 0 0 0 0 ... $ medn_cov : int 6 6 5 5 5 4 5 5 5 4 ... $ indivd : int 3 3 3 3 3 3 3 3 3 3 ... $ perc_meth_1 : num 16.7 0 0 0 0 ... $ perc_meth_2 : num 0 12.5 0 0 0 0 0 0 0 0 ... $ perc_meth_3 : num 0 0 0 20 0 0 0 20 0 0 ... $ reads_1 : int 6 6 5 5 5 4 5 5 3 4 ... $ reads_2 : int 7 8 8 8 8 10 9 10 10 10 ... $ reads_3 : int 3 3 4 5 4 4 4 5 5 4 ... $ meth_tag : chr "[0-10%]" "[0-10%]" "[0-10%]" "[0-10%]" ... $ cov_tag : chr "[5-10]" "[5-10]" "[5-10]" "[5-10]" ... $ group : chr "WGBS" "WGBS" "WGBS" "WGBS" ... $ group_simp : chr "WGBS" "WGBS" "WGBS" "WGBS" ... $ mbd_cov_tag : chr "[0]" "[0]" "[0]" "[0]" ... $ wgbs_meth_tag: chr "[0-10%]" "[0-10%]" "[0-10%]" "[0-10%]" ... MBD_RRBS_WGBS MBD_WGBS RRBS_WGBS WGBS 1310201 2739744 784106 2653619 null device 1 'data.frame': 15831344 obs. of 17 variables: $ loci : chr "1:1000005-1000007" "1:1000016-1000018" "1:1000029-1000031" "1:1000076-1000078" ... $ method : chr "WGBS" "WGBS" "WGBS" "WGBS" ... $ medn_meth : num 0 0 0 0 0 0 0 0 0 0 ... $ medn_cov : int 2 2 2 5 5 6 3 2 4 4 ... $ indivd : int 3 3 3 3 3 3 3 3 3 3 ... $ perc_meth_1 : num 0 0 0 0 0 0 0 0 0 0 ... $ perc_meth_2 : num 0 0 0 0 0 0 0 0 0 0 ... $ perc_meth_3 : num 0 0 0 0 0 ... $ reads_1 : int 2 2 1 1 1 1 1 2 4 4 ... $ reads_2 : int 2 2 2 5 5 6 3 2 3 2 ... $ reads_3 : int 4 4 3 7 7 7 5 5 6 5 ... $ meth_tag : chr "[0-10%]" "[0-10%]" "[0-10%]" "[0-10%]" ... $ cov_tag : chr "[1-5]" "[1-5]" "[1-5]" "[5-10]" ... $ group : chr "WGBS" "WGBS" "WGBS" "WGBS_MBD" ... $ group_simp : chr "WGBS" "WGBS" "WGBS" "MBD_WGBS" ... $ mbd_cov_tag : chr "[0]" "[0]" "[0]" NA ... $ wgbs_meth_tag: chr "[0-10%]" "[0-10%]" "[0-10%]" "[0-10%]" ... MBD_RRBS_WGBS MBD_WGBS RRBS_WGBS WGBS 456108 2084296 1495679 9254857 null device 1 [1] "scaffold1_cov55:119-121" "scaffold1_cov55:194-196" [3] "scaffold10_cov103:10247-10249" "scaffold10_cov103:10252-10254" [5] "scaffold10_cov103:10261-10263" "scaffold10_cov103:10307-10309" [1] "scaffold10_cov103:11870-11872" "scaffold10_cov103:11885-11887" [3] "scaffold10_cov103:11907-11909" "scaffold10_cov103:11909-11911" [5] "scaffold10_cov103:11916-11918" "scaffold10_cov103:11918-11920" [1] "scaffold10_cov103:15588-15590" "scaffold100018_cov50:114-116" [3] "scaffold100018_cov50:116-118" "scaffold100018_cov50:128-130" [5] "scaffold100018_cov50:137-139" "scaffold100018_cov50:200-202" [1] "scaffold100018_cov50:116-118" "scaffold100018_cov50:128-130" [3] "scaffold100018_cov50:137-139" "scaffold100034_cov58:103-105" [5] "scaffold100034_cov58:137-139" "scaffold100034_cov58:155-157" [1] "scaffold10006_cov97:121-123" "scaffold10006_cov97:124-126" [3] "scaffold10006_cov97:36-38" "scaffold10006_cov97:66-68" [5] "scaffold100130_cov61:393-395" "scaffold100146_cov96:120-122" [1] "scaffold10006_cov97:66-68" "scaffold100146_cov96:120-122" [3] "scaffold100146_cov96:131-133" "scaffold100146_cov96:148-150" [5] "scaffold100146_cov96:160-162" "scaffold100146_cov96:162-164" [1] "scaffold10006_cov97:66-68" "scaffold100146_cov96:120-122" [3] "scaffold100146_cov96:131-133" "scaffold100146_cov96:148-150" [5] "scaffold100146_cov96:160-162" "scaffold100146_cov96:162-164" loci group_simp mbd_cov_tag wgbs_meth_tag 1 1:1000551-1000553 RRBS_WGBS [0] [0-10%] 2 1:1000587-1000589 MBD_RRBS_WGBS [1-5] [0-10%] 3 1:1000589-1000591 MBD_RRBS_WGBS [1-5] [0-10%] 4 1:1000596-1000598 MBD_RRBS_WGBS [1-5] [0-10%] 5 1:1000602-1000604 MBD_RRBS_WGBS [1-5] [0-10%] 6 1:1000616-1000618 MBD_RRBS_WGBS [1-5] [0-10%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 1:1011444-1011446 WGBS [0] [0-10%] 2 1:1011467-1011469 WGBS [0] [0-10%] 3 1:1011470-1011472 WGBS [0] [0-10%] 4 1:1011473-1011475 WGBS [0] [0-10%] 5 1:1054206-1054208 WGBS [0] [0-10%] 6 1:1106115-1106117 MBD_WGBS [1-5] [0-10%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 1:2766725-2766727 MBD_WGBS [5-10] [0-10%] 2 100:321979-321981 MBD_WGBS [10-20] [0-10%] 3 100:321984-321986 MBD_WGBS [10-20] [0-10%] 4 100:321993-321995 MBD_WGBS [10-20] [0-10%] 5 100:321997-321999 MBD_WGBS [10-20] [0-10%] 6 100:782263-782265 MBD_RRBS_WGBS [5-10] [0-10%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 1007:262448-262450 MBD_WGBS [10-20] [0-10%] 2 1007:262450-262452 MBD_WGBS [10-20] [0-10%] 3 1007:262452-262454 MBD_WGBS [10-20] [0-10%] 4 1007:262467-262469 MBD_WGBS [10-20] [0-10%] 5 1007:262470-262472 MBD_WGBS [10-20] [0-10%] 6 1007:262542-262544 MBD_WGBS [10-20] [0-10%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 1007:262763-262765 MBD_WGBS [10-20] [0-10%] 2 1007:262808-262810 MBD_WGBS [10-20] [0-10%] 3 1007:263069-263071 MBD_WGBS [10-20] [0-10%] 4 1007:263093-263095 MBD_WGBS [5-10] [0-10%] 5 1007:263161-263163 MBD_WGBS [10-20] [0-10%] 6 102:13170-13172 MBD_RRBS_WGBS [5-10] [10-20%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 102:13286-13288 MBD_RRBS_WGBS [10-20] [0-10%] 2 102:13299-13301 MBD_RRBS_WGBS [10-20] [0-10%] 3 102:13374-13376 MBD_RRBS_WGBS [10-20] [0-10%] 4 102:13428-13430 MBD_WGBS [10-20] [0-10%] 5 102:13546-13548 MBD_WGBS [20-30] [0-10%] 6 102:13558-13560 MBD_WGBS [20-30] [0-10%] loci group_simp mbd_cov_tag wgbs_meth_tag 1 102:14288-14290 MBD_RRBS_WGBS [20-30] [0-10%] 2 1064:280931-280933 MBD_WGBS [100-500] [0-10%] 3 1064:280934-280936 MBD_WGBS [100-500] [0-10%] 4 1064:280946-280948 MBD_WGBS [100-500] [0-10%] 5 1064:280953-280955 MBD_WGBS [100-500] [0-10%] 6 1064:280983-280985 MBD_WGBS [100-500] [0-10%] # A tibble: 6 x 3 # Groups: mbd_cov_tag [1] mbd_cov_tag wgbs_meth_tag CpGs 1 [0] [0-10%] 740620 2 [0] [10-20%] 31829 3 [0] [20-30%] 14318 4 [0] [30-40%] 7632 5 [0] [40-50%] 8765 6 [0] [50-60%] 9169 # A tibble: 6 x 3 # Groups: mbd_cov_tag [1] mbd_cov_tag wgbs_meth_tag CpGs 1 [0] [0-10%] 12138 2 [0] [10-20%] 723 3 [0] [20-30%] 447 4 [0] [30-40%] 339 5 [0] [40-50%] 287 6 [0] [50-60%] 300 # A tibble: 6 x 3 # Groups: mbd_cov_tag [1] mbd_cov_tag wgbs_meth_tag CpGs 1 [0] [0-10%] 109 2 [0] [10-20%] 12 3 [0] [20-30%] 6 4 [0] [30-40%] 3 5 [0] [50-60%] 3 6 [0] [60-70%] 2 # A tibble: 6 x 3 # Groups: mbd_cov_tag [2] mbd_cov_tag wgbs_meth_tag CpGs 1 [0] [0-10%] 12 2 [1-5] [0-10%] 28 3 [1-5] [10-20%] 2 4 [1-5] [20-30%] 4 5 [1-5] [30-40%] 1 6 [1-5] [40-50%] 1 # A tibble: 6 x 3 # Groups: mbd_cov_tag [2] mbd_cov_tag wgbs_meth_tag CpGs 1 [1-5] [0-10%] 1 2 [1-5] [20-30%] 1 3 [1-5] [40-50%] 1 4 [1-5] [60-70%] 1 5 [10-20] [0-10%] 1188 6 [10-20] [10-20%] 67 # A tibble: 6 x 3 # Groups: mbd_cov_tag [1] mbd_cov_tag wgbs_meth_tag CpGs 1 [10-20] [0-10%] 602 2 [10-20] [10-20%] 37 3 [10-20] [20-30%] 8 4 [10-20] [30-40%] 8 5 [10-20] [40-50%] 5 6 [10-20] [50-60%] 3 # A tibble: 6 x 3 # Groups: mbd_cov_tag [2] mbd_cov_tag wgbs_meth_tag CpGs 1 [10-20] [0-10%] 16 2 [10-20] [40-50%] 1 3 [100-500] [0-10%] 378 4 [100-500] [10-20%] 72 5 [100-500] [20-30%] 22 6 [100-500] [30-40%] 12 null device 1 null device 1 null device 1 null device 1