Construct logical indexes for DERs and regionMatrix regions.
Number of regions
## ders regs
## 15900 180397
Summary on width of regions
## ders.Min. ders.1st Qu. ders.Median ders.Mean ders.3rd Qu.
## 3.00 4.00 7.00 12.34 14.00
## ders.Max. regs.Min. regs.1st Qu. regs.Median regs.Mean
## 182.00 3.00 12.00 36.00 56.87
## regs.3rd Qu. regs.Max.
## 70.00 5572.00
Number of base-pairs in each index. Summary first, then overall info for the genome (in number of bases, then in percent of the genome), and finally results in interactive table.
## both only.der only.reg none
## Min. : 471 Min. : 10.0 Min. : 17706 Min. : 48039170
## 1st Qu.: 4646 1st Qu.: 663.8 1st Qu.: 300546 1st Qu.: 79841586
## Median : 6343 Median : 940.0 Median : 374345 Median :133877898
## Mean : 7251 Mean : 921.5 Mean : 420243 Mean :128558143
## 3rd Qu.: 9428 3rd Qu.:1097.8 3rd Qu.: 534129 3rd Qu.:161639197
## Max. :27552 Max. :2347.0 Max. :1040506 Max. :248194137
## all.der all.reg chrLen chr
## Min. : 481 Min. : 18177 Min. : 48129895 Length:24
## 1st Qu.: 5413 1st Qu.: 304750 1st Qu.: 80415720 Class :character
## Median : 7281 Median : 381242 Median :134429206 Mode :character
## Mean : 8172 Mean : 427494 Mean :128986559
## 3rd Qu.:10670 3rd Qu.: 541522 3rd Qu.:162132764
## Max. :28918 Max. :1054137 Max. :249250621
## both only.der only.reg none all.der all.reg
## 174014 22117 10085842 3085395439 196131 10259856
## chrLen
## 3095677412
## both only.der only.reg none all.der
## 5.621193e-03 7.144478e-04 3.258040e-01 9.966786e+01 6.335641e-03
## all.reg chrLen
## 3.314252e-01 1.000000e+02
1 | 13631 | 2347 | 1040506 | 248194137 | 15978 | 1054137 | 249250621 | chr1 |
2 | 9369 | 1547 | 645106 | 242543351 | 10916 | 654475 | 243199373 | chr2 |
3 | 7397 | 1022 | 471182 | 197542829 | 8419 | 478579 | 198022430 | chr3 |
4 | 4898 | 805 | 288974 | 190859599 | 5703 | 293872 | 191154276 | chr4 |
5 | 6806 | 1346 | 446797 | 180460311 | 8152 | 453603 | 180915260 | chr5 |
6 | 7438 | 1009 | 398214 | 170708406 | 8447 | 405652 | 171115067 | chr6 |
7 | 6655 | 1181 | 514700 | 158616127 | 7836 | 521355 | 159138663 | chr7 |
8 | 5302 | 793 | 285643 | 146072284 | 6095 | 290945 | 146364022 | chr8 |
9 | 6031 | 695 | 412848 | 140793857 | 6726 | 418879 | 141213431 | chr9 |
10 | 5796 | 854 | 350476 | 135177621 | 6650 | 356272 | 135534747 | chr10 |
11 | 9606 | 1014 | 592415 | 134403481 | 10620 | 602021 | 135006516 | chr11 |
12 | 11328 | 1031 | 487221 | 133352315 | 12359 | 498549 | 133851895 | chr12 |
13 | 1907 | 446 | 134496 | 115033029 | 2353 | 136403 | 115169878 | chr13 |
14 | 4912 | 869 | 308150 | 107035609 | 5781 | 313062 | 107349540 | chr14 |
15 | 4871 | 871 | 323103 | 102202547 | 5742 | 327974 | 102531392 | chr15 |
16 | 7976 | 1070 | 601264 | 89744443 | 9046 | 609240 | 90354753 | chr16 |
17 | 11288 | 1182 | 710391 | 80472349 | 12470 | 721679 | 81195210 | chr17 |
18 | 1481 | 300 | 126170 | 77949297 | 1781 | 127651 | 78077248 | chr18 |
19 | 27552 | 1366 | 847232 | 58252833 | 28918 | 874784 | 59128983 | chr19 |
20 | 3972 | 570 | 304404 | 62716574 | 4542 | 308376 | 63025520 | chr20 |
21 | 1631 | 232 | 88862 | 48039170 | 1863 | 90493 | 48129895 | chr21 |
22 | 3896 | 539 | 342951 | 50957180 | 4435 | 346847 | 51304566 | chr22 |
23 | 9800 | 1018 | 347031 | 154912711 | 10818 | 356831 | 155270560 | chrX |
24 | 471 | 10 | 17706 | 59355379 | 481 | 18177 | 59373566 | chrY |
Number of segments per index. First summary, then results for genome, and finally an interactive table.
## both only.der only.reg none
## Min. : 26.0 Min. : 2.0 Min. : 391 Min. : 372
## 1st Qu.: 357.5 1st Qu.:113.2 1st Qu.: 5697 1st Qu.: 5486
## Median : 508.0 Median :136.5 Median : 7558 Median : 7276
## Mean : 546.9 Mean :143.9 Mean : 7978 Mean : 7627
## 3rd Qu.: 694.2 3rd Qu.:171.2 3rd Qu.:10105 3rd Qu.: 9745
## Max. :1726.0 Max. :372.0 Max. :19596 Max. :18908
## all.der all.reg chr
## Min. : 28.0 Min. : 369 Length:24
## 1st Qu.: 456.0 1st Qu.: 5410 Class :character
## Median : 623.5 Median : 7158 Mode :character
## Mean : 662.5 Mean : 7517
## 3rd Qu.: 808.8 3rd Qu.: 9615
## Max. :1885.0 Max. :18604
## both only.der only.reg none all.der all.reg
## 13125 3454 191474 183045 15900 180397
1 | 1152 | 372 | 19596 | 18908 | 1473 | 18604 | chr1 |
2 | 796 | 228 | 12813 | 12331 | 977 | 12157 | chr2 |
3 | 568 | 157 | 9745 | 9380 | 701 | 9251 | chr3 |
4 | 392 | 128 | 6234 | 6019 | 495 | 5918 | chr4 |
5 | 532 | 175 | 8434 | 8134 | 685 | 7985 | chr5 |
6 | 502 | 162 | 7885 | 7595 | 638 | 7467 | chr6 |
7 | 555 | 170 | 9868 | 9563 | 696 | 9425 | chr7 |
8 | 412 | 122 | 5534 | 5288 | 514 | 5192 | chr8 |
9 | 514 | 119 | 7937 | 7598 | 609 | 7505 | chr9 |
10 | 440 | 134 | 7232 | 6958 | 554 | 6850 | chr10 |
11 | 758 | 166 | 10816 | 10292 | 877 | 10184 | chr11 |
12 | 779 | 161 | 9468 | 8983 | 914 | 8852 | chr12 |
13 | 130 | 69 | 2932 | 2889 | 193 | 2828 | chr13 |
14 | 364 | 126 | 5880 | 5675 | 468 | 5576 | chr14 |
15 | 419 | 122 | 6551 | 6304 | 522 | 6202 | chr15 |
16 | 673 | 175 | 11543 | 11082 | 786 | 10972 | chr16 |
17 | 821 | 195 | 12729 | 12175 | 984 | 12019 | chr17 |
18 | 153 | 46 | 2632 | 2539 | 189 | 2505 | chr18 |
19 | 1726 | 266 | 14097 | 12734 | 1885 | 12593 | chr19 |
20 | 338 | 96 | 5253 | 5040 | 420 | 4960 | chr20 |
21 | 129 | 34 | 1745 | 1659 | 155 | 1635 | chr21 |
22 | 335 | 90 | 5751 | 5552 | 407 | 5482 | chr22 |
23 | 611 | 139 | 6408 | 5975 | 730 | 5866 | chrX |
24 | 26 | 2 | 391 | 372 | 28 | 369 | chrY |
Summary of the segment widths for each index. First the overall summary, then the results for each index.
## Min. 1st Qu. Median Mean
## Min. :1.000 Min. : 3.00 Min. : 4.00 Min. : 5.00
## 1st Qu.:1.000 1st Qu.: 4.00 1st Qu.: 6.00 1st Qu.: 11.63
## Median :1.000 Median : 8.00 Median : 23.00 Median : 31.70
## Mean :1.694 Mean : 8.26 Mean : 33.74 Mean : 4198.87
## 3rd Qu.:3.000 3rd Qu.:12.00 3rd Qu.: 36.00 3rd Qu.: 56.19
## Max. :3.000 Max. :39.75 Max. :259.00 Max. :159600.00
## 3rd Qu. Max. index
## Min. : 6.00 Min. : 7 Length:144
## 1st Qu.: 13.00 1st Qu.: 98 Class :character
## Median : 44.25 Median : 307 Mode :character
## Mean : 276.39 Mean : 1609538
## 3rd Qu.: 70.00 3rd Qu.: 2746
## Max. :3379.00 Max. :30260000
## chr
## Length:144
## Class :character
## Mode :character
##
##
##
1 | 1 | 4 | 7 | 11.83 | 14 | 105 | both | chr1 |
2 | 1 | 3 | 4 | 6.309 | 8 | 27 | only.der | chr1 |
3 | 1 | 11 | 35 | 53.1 | 68 | 2168 | only.reg | chr1 |
4 | 1 | 14 | 104 | 13130 | 1090 | 21230000 | none | chr1 |
5 | 3 | 4 | 6 | 10.85 | 13 | 105 | all.der | chr1 |
6 | 3 | 12 | 36 | 56.66 | 71 | 2698 | all.reg | chr1 |
7 | 1 | 4 | 7 | 11.77 | 14 | 129 | both | chr2 |
8 | 1 | 3 | 5 | 6.785 | 8 | 28 | only.der | chr2 |
9 | 1 | 11 | 34 | 50.35 | 63 | 1581 | only.reg | chr2 |
10 | 1 | 14 | 103 | 19670 | 1462 | 3462000 | none | chr2 |
11 | 3 | 4 | 7 | 11.17 | 13 | 129 | all.der | chr2 |
12 | 3 | 12 | 35 | 53.84 | 66 | 3227 | all.reg | chr2 |
13 | 1 | 4 | 7 | 13.02 | 16.25 | 143 | both | chr3 |
14 | 1 | 3 | 5 | 6.51 | 8 | 33 | only.der | chr3 |
15 | 1 | 10 | 33 | 48.35 | 61 | 1274 | only.reg | chr3 |
16 | 1 | 13 | 106 | 21060 | 1470 | 4919000 | none | chr3 |
17 | 3 | 4 | 6 | 12.01 | 15 | 143 | all.der | chr3 |
18 | 3 | 11 | 34 | 51.73 | 64 | 1548 | all.reg | chr3 |
19 | 1 | 4 | 7 | 12.49 | 15 | 97 | both | chr4 |
20 | 1 | 3 | 5 | 6.289 | 8 | 27 | only.der | chr4 |
21 | 1 | 11 | 33 | 46.35 | 55 | 1853 | only.reg | chr4 |
22 | 1 | 16 | 134 | 31710 | 1963 | 4920000 | none | chr4 |
23 | 3 | 4 | 7 | 11.52 | 13 | 97 | all.der | chr4 |
24 | 3 | 12 | 34 | 49.66 | 58 | 1853 | all.reg | chr4 |
25 | 1 | 4 | 7 | 12.79 | 14 | 100 | both | chr5 |
Summary plots showing cumulative frequency and cumulative percent.
Some important numbers: percent of regions with width < 20 bp, base level agreement, region level agreement (min overlap 20 bp).
## under-20 20-and-above
## ders 82.43396 17.56604
## regs 34.13582 65.86418
## regs.both ders.both
## 1.696067 88.723353
## regs ders
## 1.139709 16.578616
Summary plots showing cumulative frequency and cumulative percent.
Analysis path: /dcl01/lieber/ajaffe/derRuns/derSoftware/hippo/regionMatrix-vs-DERs/cut3-vs-run3-v1.0.10
Re-make the report
Date the report was generated.
## [1] "2014-11-23 18:06:46 EST"
R
session information.
## setting value
## version R version 3.1.1 Patched (2014-10-16 r66782)
## system x86_64, linux-gnu
## ui X11
## language (EN)
## collate en_US.UTF-8
## tz
## package * version date source
## BiocGenerics * 0.12.1 2014-11-15 Bioconductor
## Cairo 1.5.6 2014-06-26 CRAN (R 3.1.0)
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## GenomicRanges * 1.18.3 2014-11-20 Bioconductor
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## knitrBootstrap * 1.0.0 2014-11-19 Github (jimhester/knitrBootstrap@76c41f0)
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## yaml 2.1.13 2014-06-12 CRAN (R 3.1.1)