vignettes/plotAnnot.md
In charles-plessy/smallCAGEqc: ad-hoc QC functions for shallow-sequenced test CAGE libraries
Annotation plots with smallCAGEqc
Charles Plessy
r Sys.Date()
R commands
The main command to produce annotation plots in smallCAGEqc is called
plotAnnot. It takes a table containing the sample metadata, a scope,
a title and optionally a factor to group similar plots together.
The scope determines what data is plotted and how it is normalised.
The available scopes will be explained with an example plot in a later part
of this document, but first, let's see the input in more details.
Here, we will use some of the example data that is distributed in smallCAGEqc.
The commands below load the R package and load the example data in a data frame
called libs.
library(smallCAGEqc)
libs <- read.table(system.file("extdata/libs-with-all-metadata.tsv", package="smallCAGEqc"))
Sample metadata
The following columns in the metadata table describe the total remaining pairs
step after step in the processing.
-
total: The total number of pairs before tag extraction (called "raw" in
some other pipelines). In cases where this number is not available per sample,
for example when demultiplexing and tag extraction are performed at the same
stage, it is set arbitrarily to zero.
-
extracted: The number of pairs where the linkers and unique molecular
identifier (if present) were successfully extracted.
-
cleaned: The number of pairs remaining after filtering out spike, rRNA,
low-complexity, primer artefact and other unwanted sequences.
-
mapped: The number of pairs with at least one successful alignment. This
called "genome_mapped" in some other pipelines.
-
properpairs: The number or pair remaining after filtering out the
non-proper alignments. This is called "properly_mapped" in some other
pipelines.
-
counts: The number of unique molecules counted after alignment. This is
called "transcript_count" in some other pipelines.
The following columns describe the number of pairs removed at some step of
the processing.
-
spikes, rdna: The number of pairs removed because they matched
spikes or rRNA reference sequences, respectively.
-
tagdust: The number of pairs removed because of low-complexity or
similarity to primer artefacts.
The following columns describe the number of TSS (after proper pairing and
deduplication) aligning to known regions in the genome.
-
promoter: Promoter regions.
-
exon: Known exons.
-
intron: Know introns (that is: the TSS matches a transcript but none of
its exons).
-
unknown: None of the above; basically intergenic.
-
other: Normally there should not be anything in this category since
unknown should catch all intergenic TSS. But sometimes there is a
misdesign, for instance in the example data here, the annotation file
contained one more category, "boundary", which was not handled correctly
by smallCAGEqc.
The annotation is hierarchical (promoters have priority on exons, etc.), so
the sum of the annotation columns above should be be equal to the counts
column.
Different types of scopes
Step-by-step extraction
Shows how many pairs are removed by the extraction, cleaning, mapping
(proper pairs) and transcript counting steps described above.
-
Extraction: The total number of pairs where a tag could not be extracted
(extracted - cleaned).
-
Cleaning: The total number of pairs where a tag was discarded because
it matched a reference or artefact sequence, or because it had low complexity
(tagdust + rdna + spikes, or cleaned - mapped).
-
Mapping: The number of non-mapped pairs (mapped - properpairs).
-
Deduplication: The number of non-properly mapped pairs (properpairs -
counts).
-
Counts: The number of molecule counts.
plotAnnot(libs, "steps", "steps")
QC report
Pairs are categorised as tag dust, rDNA, spikes, unmapped, non-proper,
duplicates and counts, and normalised by the total number of extracted pairs.
Non-extracted pairs are ignored.
Compared to "steps", this scope gives more details on the sequences removed
at the TagDust and mapping stages of the processing pipeline.
-
Tag_dust, rDNA, Spikes: same numbers as in the tagdust, rdna
and spikes columns of the metadata table.
-
Unmapped: The number of pairs that could not be mapped.
-
Non_proper: The number of pairs that did not have a proper alignment.
-
Duplicates: The number of pairs that do not add a molecule count.
-
Counts: same as in "steps".
plotAnnot(libs, "qc", "qc")
Annotation of the transcript or tag counts
The unique molecule counts are grouped in annotation categories
("promoter", "exon", "intron" and "intergenic"), as described above.
plotAnnot(libs[libs$counts > 0,], "counts", "counts")
Annotation of the mapped reads
Same as "counts", with the addition of duplicates and non-proper pairs.
Therefore the plot represents all the mapped data.
plotAnnot(libs, "mapped", "mapped")
QC including annotations
Pairs are categorised by extraction step and genome annotation.
plotAnnot(libs, "all", "all")
Annotation, normalised by mapped reads
Same as all except that normalisation is relative to the number of mapped reads
plotAnnot(libs, "annotation", "annotation")
Contents of the libs table
libs
## samplename sampleid total extracted cleaned tagdust rdna spikes
## A01 A01 1 57836 44740 33456 11244 40 0
## A02 A02 2 56608 42798 31358 11404 36 0
## A03 A03 3 79068 60769 49450 11283 36 0
## A04 A04 4 51895 37394 26998 10356 40 0
## A05 A05 5 62074 45786 34516 11239 31 0
## A06 A06 6 44003 29504 21978 7471 55 0
## A07 A07 7 60988 42773 28707 14026 40 0
## A08 A08 8 32950 23815 17276 6508 31 0
## A09 A09 9 28039 21889 15656 6163 70 0
## A10 A10 10 33938 24986 18511 6455 20 0
## A11 A11 11 31996 24512 16077 8352 83 0
## A12 A12 12 31146 24500 16029 8435 36 0
## B01 B01 13 113516 79890 47354 6246 26290 0
## B02 B02 14 72654 50406 31768 4061 14577 0
## B03 B03 15 106809 62736 50864 6573 5299 0
## B04 B04 16 80569 47843 34153 6099 7591 0
## B05 B05 17 107056 65211 48808 6118 10285 0
## B06 B06 18 79748 43397 30860 4525 8012 0
## B07 B07 19 110920 65635 51751 4582 9302 0
## B08 B08 20 66320 45432 28835 6448 10149 0
## B09 B09 21 95686 62955 40331 4706 17918 0
## B10 B10 22 55199 33872 18625 5643 9604 0
## B11 B11 23 48259 30849 21371 4268 5210 0
## B12 B12 24 72900 46406 26727 4635 15044 0
## C01 C01 25 149338 89401 49290 7319 32792 0
## C02 C02 26 138463 88758 63852 2770 22136 0
## C03 C03 27 129733 84172 49076 4081 31015 0
## C04 C04 28 110834 65837 49627 3515 12695 0
## C05 C05 29 143846 78132 53696 4636 19800 0
## C06 C06 30 109061 68825 38230 5636 24959 0
## C07 C07 31 119133 75078 44183 3683 27212 0
## C08 C08 32 78937 50912 33410 3141 14361 0
## C09 C09 33 92263 57695 35157 4207 18331 0
## C10 C10 34 104621 64239 47782 3627 12830 0
## C11 C11 35 77071 43272 31482 2827 8963 0
## C12 C12 36 75814 44190 34379 2762 7049 0
## D01 D01 37 211918 108057 93175 687 14195 0
## D02 D02 38 126215 72882 61995 446 10441 0
## D03 D03 39 141855 72767 59564 392 12811 0
## D04 D04 40 176145 89332 79117 443 9772 0
## D05 D05 41 175940 86247 74584 587 11076 0
## D06 D06 42 121366 62256 53868 519 7868 1
## D07 D07 43 121058 61880 51964 503 9413 0
## D08 D08 44 72706 36161 29710 397 6054 0
## D09 D09 45 97847 42801 33270 371 9160 0
## D10 D10 46 100807 54161 46082 400 7679 0
## D11 D11 47 108622 53295 47374 470 5450 1
## D12 D12 48 128301 62093 54183 339 7571 0
## E01 E01 49 198156 114073 101593 262 12215 3
## E02 E02 50 110978 56915 50023 194 6698 0
## E03 E03 51 115523 59100 52904 219 5977 0
## E04 E04 52 64343 32652 29219 63 3370 0
## E05 E05 53 133978 64977 58020 281 6676 0
## E06 E06 54 110519 54552 48413 208 5930 1
## E07 E07 55 102993 52575 46403 215 5957 0
## E08 E08 56 88876 42892 39408 200 3282 2
## E09 E09 57 84478 36919 33088 145 3685 1
## E10 E10 58 98540 47225 41223 425 5577 0
## E11 E11 59 94995 48522 42903 193 5425 1
## E12 E12 60 59296 34992 31704 131 3157 0
## F01 F01 61 133894 69445 64738 179 4528 0
## F02 F02 62 104592 52786 49382 143 3260 1
## F03 F03 63 105865 56012 53310 194 2508 0
## F04 F04 64 151032 70854 67432 160 3262 0
## F05 F05 65 133736 62248 58816 203 3229 0
## F06 F06 66 112267 49548 47160 88 2298 2
## F07 F07 67 120527 56568 52913 192 3463 0
## F08 F08 68 81028 36749 34530 155 2064 0
## F09 F09 69 82247 37776 35593 208 1975 0
## F10 F10 70 116168 53753 50827 170 2755 1
## F11 F11 71 85752 41126 39325 168 1633 0
## F12 F12 72 96754 40894 39065 159 1670 0
## G01 G01 73 157245 77357 73610 185 3560 2
## G02 G02 74 140353 64494 61409 162 2923 0
## G03 G03 75 106273 48053 45657 214 2182 0
## G04 G04 76 161767 70158 67226 196 2736 0
## G05 G05 77 111602 48539 46504 151 1883 1
## G06 G06 78 145265 61302 58751 155 2396 0
## G07 G07 79 170602 68849 66149 272 2428 0
## G08 G08 80 85777 36517 34632 149 1736 0
## G09 G09 81 87382 34965 33038 171 1755 1
## G10 G10 82 80439 29017 28083 183 751 0
## G11 G11 83 76145 32785 31503 128 1153 1
## G12 G12 84 91108 35631 33763 169 1699 0
## H01 H01 85 167121 75412 72015 252 3145 0
## H02 H02 86 134912 59559 57087 148 2324 0
## H03 H03 87 98710 44567 42472 241 1854 0
## H04 H04 88 144495 58339 56288 204 1847 0
## H05 H05 89 129765 43742 41949 336 1457 0
## H06 H06 90 113057 42409 39991 139 2279 0
## H07 H07 91 176644 66278 63319 240 2719 0
## H08 H08 92 98958 34662 33525 196 941 0
## H09 H09 93 83042 29701 28537 171 993 0
## H10 H10 94 66452 20773 19790 81 902 0
## H11 H11 95 89280 27906 26841 166 899 0
## H12 H12 96 83539 28756 27666 148 942 0
## mapped properpairs counts group group_alpha row col Concentration
## A01 16191 161 128 0 0.000 1 A 0.162
## A02 15558 166 123 0 0.000 2 A 0.176
## A03 21330 211 159 0 0.000 3 A 0.162
## A04 11657 226 164 0 0.000 4 A 0.137
## A05 18286 291 215 0 0.000 5 A 0.152
## A06 10913 149 111 0 0.000 6 A 0.167
## A07 10873 0 0 0 0.000 7 A 0.177
## A08 8403 126 105 0 0.000 8 A 0.184
## A09 6973 135 98 0 0.000 9 A 0.208
## A10 9937 120 109 0 0.000 10 A 0.153
## A11 7830 208 126 0 0.000 11 A 0.161
## A12 7225 129 102 0 0.000 12 A 0.155
## B01 37640 22667 14343 5 0.005 1 B 0.156
## B02 24362 13744 7537 5 0.005 2 B 0.197
## B03 41386 17864 12282 5 0.005 3 B 0.203
## B04 26392 17496 11951 5 0.005 4 B 0.160
## B05 42219 23383 14708 5 0.005 5 B 0.154
## B06 26235 16390 9672 5 0.005 6 B 0.186
## B07 45950 27813 14672 5 0.005 7 B 0.243
## B08 23143 13753 8318 5 0.005 8 B 0.065
## B09 35094 20483 11170 5 0.005 9 B 0.230
## B10 13506 6561 3603 5 0.005 10 B 0.145
## B11 15098 7019 4573 5 0.005 11 B 0.145
## B12 21986 9790 5586 5 0.005 12 B 0.190
## C01 41268 27344 15537 10 0.010 1 C 0.247
## C02 59641 43036 29995 10 0.010 2 C 0.348
## C03 43278 34189 22366 10 0.010 3 C 0.235
## C04 45103 33171 19651 10 0.010 4 C 0.217
## C05 49398 30795 20012 10 0.010 5 C 0.267
## C06 34091 24496 18016 10 0.010 6 C 0.235
## C07 40045 29773 21171 10 0.010 7 C 0.155
## C08 29481 21380 14386 10 0.010 8 C 0.090
## C09 31130 22610 15230 10 0.010 9 C 0.276
## C10 42111 30183 20526 10 0.010 10 C 0.320
## C11 27613 18027 13697 10 0.010 11 C 0.223
## C12 30804 20590 13729 10 0.010 12 C 0.297
## D01 89865 65730 52248 50 0.050 1 D 0.530
## D02 60842 45193 34407 50 0.050 2 D 0.542
## D03 58729 47380 36083 50 0.050 3 D 0.620
## D04 77923 60089 44735 50 0.050 4 D 0.527
## D05 72447 56669 43199 50 0.050 5 D 0.497
## D06 52333 39002 31387 50 0.050 6 D 0.568
## D07 50824 39326 31103 50 0.050 7 D 0.771
## D08 28976 22389 18234 50 0.050 8 D 0.690
## D09 32704 24638 19555 50 0.050 9 D 0.616
## D10 44784 34443 27639 50 0.050 10 D 0.478
## D11 46716 35769 27793 50 0.050 11 D 0.604
## D12 53167 41331 33085 50 0.050 12 D 0.636
## E01 99997 79165 62741 100 0.100 1 E 0.472
## E02 48990 37058 30889 100 0.100 2 E 0.616
## E03 51701 41228 33789 100 0.100 3 E 0.633
## E04 28879 20711 17324 100 0.100 4 E 0.577
## E05 57053 44186 36254 100 0.100 5 E 0.523
## E06 47367 34363 28622 100 0.100 6 E 0.669
## E07 45657 34766 28742 100 0.100 7 E 0.802
## E08 38534 28422 23454 100 0.100 8 E 0.724
## E09 32387 23970 20526 100 0.100 9 E 0.606
## E10 39997 30301 27506 100 0.100 10 E 0.451
## E11 42451 32153 26738 100 0.100 11 E 0.614
## E12 31410 24025 20323 100 0.100 12 E 0.668
## F01 63961 49002 41263 500 0.500 1 F 0.974
## F02 48692 38696 32393 500 0.500 2 F 0.718
## F03 52663 40504 34118 500 0.500 3 F 0.723
## F04 66550 51626 43342 500 0.500 4 F 0.719
## F05 57743 43906 37310 500 0.500 5 F 0.720
## F06 46529 36544 31401 500 0.500 6 F 0.903
## F07 52396 40338 33918 500 0.500 7 F 0.887
## F08 34156 25786 22086 500 0.500 8 F 1.016
## F09 35174 26843 22878 500 0.500 9 F 1.009
## F10 50011 38554 32330 500 0.500 10 F 0.754
## F11 38810 29784 25397 500 0.500 11 F 0.871
## F12 38666 29332 25302 500 0.500 12 F 0.677
## G01 72874 56189 46184 1000 1.000 1 G 1.053
## G02 60664 45441 37084 1000 1.000 2 G 0.929
## G03 45000 33837 28132 1000 1.000 3 G 0.908
## G04 66289 51171 42594 1000 1.000 4 G 0.883
## G05 45715 35589 29503 1000 1.000 5 G 0.942
## G06 58119 43708 36940 1000 1.000 6 G 1.056
## G07 64834 47451 39214 1000 1.000 7 G 1.178
## G08 34114 24866 21295 1000 1.000 8 G 1.067
## G09 32645 23779 20003 1000 1.000 9 G 1.108
## G10 27695 20601 19151 1000 1.000 10 G 0.960
## G11 31184 24414 21011 1000 1.000 11 G 1.150
## G12 33260 25400 21678 1000 1.000 12 G 0.872
## H01 71031 53719 42839 2000 2.000 1 H 1.678
## H02 56441 43344 34846 2000 2.000 2 H 1.278
## H03 41591 31472 25730 2000 2.000 3 H 1.588
## H04 55498 43738 35853 2000 2.000 4 H 1.439
## H05 41274 31941 29084 2000 2.000 5 H 1.559
## H06 39554 31613 26223 2000 2.000 6 H 1.834
## H07 62372 45835 36225 2000 2.000 7 H 1.901
## H08 33016 25111 21283 2000 2.000 8 H 1.695
## H09 28126 20602 17633 2000 2.000 9 H 1.236
## H10 19449 14311 12514 2000 2.000 10 H 1.529
## H11 26455 20579 17642 2000 2.000 11 H 1.421
## H12 27106 21307 18492 2000 2.000 12 H 1.525
## Run l1 r100l1 exon intron other promoter unknown genes
## A01 1772-087-069 40 35.00393 2 42 0 10 74 12
## A02 1772-087-069 39 34.53797 0 38 0 9 76 10
## A03 1772-087-069 49 38.12546 7 36 0 12 104 16
## A04 1772-087-069 50 37.21116 0 46 0 7 111 15
## A05 1772-087-069 53 35.38931 6 49 0 31 129 20
## A06 1772-087-069 38 35.65686 1 35 0 9 66 11
## A07 1772-087-069 0 0.00000 0 0 0 0 0 0
## A08 1772-087-069 37 35.94311 2 24 0 19 60 13
## A09 1772-087-069 30 30.00000 2 16 0 3 77 9
## A10 1772-087-069 35 33.54695 2 21 0 12 74 8
## A11 1772-087-069 62 53.58818 17 21 0 16 72 22
## A12 1772-087-069 37 36.62609 1 30 0 2 69 10
## B01 1772-087-069 106 14.64366 6204 335 0 1938 5866 38
## B02 1772-087-069 290 19.19440 1926 419 0 4040 1152 80
## B03 1772-087-069 142 17.20786 179 261 0 6122 5720 30
## B04 1772-087-069 154 18.44604 1834 2255 0 4921 2941 51
## B05 1772-087-069 134 16.75237 132 786 0 2388 11402 31
## B06 1772-087-069 159 19.54335 365 2462 0 1466 5379 43
## B07 1772-087-069 211 18.26080 3529 636 0 2961 7546 53
## B08 1772-087-069 152 19.59785 17 2366 0 2154 3781 39
## B09 1772-087-069 344 28.23019 14 1154 0 1840 8162 40
## B10 1772-087-069 124 21.74362 66 1213 0 785 1539 37
## B11 1772-087-069 116 13.26322 1344 64 0 389 2776 24
## B12 1772-087-069 162 20.94065 64 1214 0 1563 2745 42
## C01 1772-087-069 242 25.48931 160 3797 0 2821 8759 61
## C02 1772-087-069 402 32.73442 971 7466 0 10701 10857 84
## C03 1772-087-069 305 27.92000 4783 6179 0 3044 8360 76
## C04 1772-087-069 370 31.87616 1798 1200 0 3225 13428 81
## C05 1772-087-069 440 31.36962 1199 5118 0 4552 9143 116
## C06 1772-087-069 212 22.82430 1817 579 0 7720 7900 59
## C07 1772-087-069 360 38.94175 2403 1797 1 5564 11406 93
## C08 1772-087-069 280 32.94986 2075 4031 3 3589 4688 70
## C09 1772-087-069 276 23.03263 293 3485 0 2464 8988 81
## C10 1772-087-069 417 45.88426 3744 5515 0 3529 7738 138
## C11 1772-087-069 241 27.15281 2437 1929 0 2658 6673 59
## C12 1772-087-069 293 28.72867 1261 3338 0 1090 8040 80
## D01 1772-087-069 1448 73.93816 6003 9940 0 9260 27045 348
## D02 1772-087-069 1405 77.98528 3542 8960 0 5350 16555 340
## D03 1772-087-069 1379 74.17269 2642 9327 0 4804 19310 300
## D04 1772-087-069 1581 76.47927 4336 9913 0 7374 23112 366
## D05 1772-087-069 1869 79.00155 2869 11857 0 4877 23596 394
## D06 1772-087-069 1715 78.34378 1972 7444 1 4598 17372 399
## D07 1772-087-069 1198 72.20326 3211 6987 0 5560 15345 296
## D08 1772-087-069 1002 72.18696 2923 4015 0 3575 7721 260
## D09 1772-087-069 1005 72.88108 2479 4706 0 2412 9958 270
## D10 1772-087-069 1507 78.98770 2867 6133 0 3407 15232 393
## D11 1772-087-069 1379 77.20211 2263 6242 1 3720 15567 337
## D12 1772-087-069 1392 77.06525 3876 8104 0 3738 17367 339
## E01 1772-087-069 2265 85.16074 5622 15233 0 7352 34534 556
## E02 1772-087-069 1900 85.41793 2566 7968 0 4010 16345 458
## E03 1772-087-069 1842 84.26035 3321 8877 0 4517 17073 466
## E04 1772-087-069 1658 85.84360 1608 4630 0 1513 9573 449
## E05 1772-087-069 2378 87.09019 3630 9858 0 3804 18962 559
## E06 1772-087-069 2138 87.99389 1837 5630 35 3990 17130 541
## E07 1772-087-069 1924 86.41941 2197 7446 0 3399 15700 497
## E08 1772-087-069 1765 86.77928 2110 5009 0 2402 13933 472
## E09 1772-087-069 1723 87.35975 2255 4181 2 2895 11193 483
## E10 1772-087-069 1793 85.70211 3102 6129 0 4647 13628 501
## E11 1772-087-069 1925 86.98539 2419 6827 1 3573 13918 507
## E12 1772-087-069 1814 87.78132 1325 4795 5 2504 11694 481
## F01 1772-087-069 3635 92.62051 4607 9108 4 3963 23581 917
## F02 1772-087-069 3358 92.82644 2575 8424 0 2852 18542 817
## F03 1772-087-069 3563 93.57936 3014 7998 0 3717 19389 854
## F04 1772-087-069 4136 93.90090 3620 9944 0 4850 24928 982
## F05 1772-087-069 3837 93.98819 3379 8444 1 4408 21078 930
## F06 1772-087-069 3741 93.91198 2160 7017 62 3832 18330 888
## F07 1772-087-069 3819 94.19979 3466 8135 0 3976 18341 951
## F08 1772-087-069 3155 94.12737 1746 5710 0 3014 11616 842
## F09 1772-087-069 3691 94.74871 2216 5101 23 2702 12836 967
## F10 1772-087-069 3615 92.98439 2627 7025 1 2741 19936 816
## F11 1772-087-069 3532 93.98666 1875 6082 0 2950 14490 932
## F12 1772-087-069 3669 94.64871 2066 6055 0 2218 14963 962
## G01 1772-087-069 4439 94.46853 4186 10762 39 6198 24999 1038
## G02 1772-087-069 4053 92.75496 3855 8373 0 3806 21050 949
## G03 1772-087-069 3752 93.66966 2697 7029 2 2832 15572 903
## G04 1772-087-069 3900 92.09875 4283 9929 0 4208 24174 850
## G05 1772-087-069 3356 92.67858 2740 6714 0 2979 17070 775
## G06 1772-087-069 3873 92.82608 3718 9021 0 4142 20059 914
## G07 1772-087-069 5138 94.78783 3631 9264 2 5200 21117 1242
## G08 1772-087-069 3977 94.43834 2051 5135 0 3144 10965 1080
## G09 1772-087-069 3806 95.08377 1742 4376 0 2667 11218 1024
## G10 1772-087-069 2642 92.13822 1432 4437 1 1757 11524 636
## G11 1772-087-069 3136 93.63214 1756 4911 0 2883 11461 800
## G12 1772-087-069 3411 94.58613 1795 4978 3 2374 12528 869
## H01 1772-087-069 4296 92.15265 4700 9467 7 4900 23765 980
## H02 1772-087-069 3697 93.16116 3503 8810 119 4394 18020 863
## H03 1772-087-069 3260 92.42869 2731 5836 0 2818 14345 802
## H04 1772-087-069 3112 90.11942 3835 7867 1 4015 20135 684
## H05 1772-087-069 2847 88.82836 3141 5493 1 3349 17100 677
## H06 1772-087-069 2671 85.46402 3499 5371 1 2258 15094 601
## H07 1772-087-069 4125 89.92747 4114 7256 0 3854 21001 934
## H08 1772-087-069 3086 92.93838 2827 5158 24 2465 10809 844
## H09 1772-087-069 3581 93.04251 2007 3820 0 2580 9226 986
## H10 1772-087-069 2565 93.39395 1287 3116 0 1515 6596 700
## H11 1772-087-069 2491 90.60411 1498 3957 0 2038 10149 595
## H12 1772-087-069 2738 91.97103 2105 4229 0 1751 10407 637
R session info
sessionInfo()
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
##
## locale:
## [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.utf8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.utf8
## [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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] smallCAGEqc_0.12.2.99999 magrittr_1.5
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.2 knitr_1.13 munsell_0.4.2
## [4] lattice_0.20-29 colorspace_1.2-6 stringr_1.0.0
## [7] plyr_1.8.3 tools_3.3.1 grid_3.3.1
## [10] gtable_0.1.2 vegan_2.0-10 lambda.r_1.1.7
## [13] futile.logger_1.4.1 htmltools_0.2.6 gtools_3.5.0
## [16] yaml_2.1.13 digest_0.6.8 permute_0.8-3
## [19] ggplot2_2.1.0 formatR_1.4 futile.options_1.0.0
## [22] VennDiagram_1.6.16 evaluate_0.8 rmarkdown_0.9.6
## [25] labeling_0.3 gdata_2.17.0 stringi_1.0-1
## [28] scales_0.4.0 reshape_0.8.5
charles-plessy/smallCAGEqc documentation built on May 13, 2019, 3:31 p.m.
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Annotation plots with smallCAGEqc
Charles Plessy
r Sys.Date()
R commands
The main command to produce annotation plots in smallCAGEqc is called
plotAnnot. It takes a table containing the sample metadata, a scope,
a title and optionally a factor to group similar plots together.
The scope determines what data is plotted and how it is normalised. The available scopes will be explained with an example plot in a later part of this document, but first, let's see the input in more details.
Here, we will use some of the example data that is distributed in smallCAGEqc.
The commands below load the R package and load the example data in a data frame
called libs.
library(smallCAGEqc)
libs <- read.table(system.file("extdata/libs-with-all-metadata.tsv", package="smallCAGEqc"))
Sample metadata
The following columns in the metadata table describe the total remaining pairs step after step in the processing.
-
total: The total number of pairs before tag extraction (called "raw" in some other pipelines). In cases where this number is not available per sample, for example when demultiplexing and tag extraction are performed at the same stage, it is set arbitrarily to zero.
-
extracted: The number of pairs where the linkers and unique molecular identifier (if present) were successfully extracted.
-
cleaned: The number of pairs remaining after filtering out spike, rRNA, low-complexity, primer artefact and other unwanted sequences.
-
mapped: The number of pairs with at least one successful alignment. This called "genome_mapped" in some other pipelines.
-
properpairs: The number or pair remaining after filtering out the non-proper alignments. This is called "properly_mapped" in some other pipelines.
-
counts: The number of unique molecules counted after alignment. This is called "transcript_count" in some other pipelines.
The following columns describe the number of pairs removed at some step of the processing.
-
spikes, rdna: The number of pairs removed because they matched spikes or rRNA reference sequences, respectively.
-
tagdust: The number of pairs removed because of low-complexity or similarity to primer artefacts.
The following columns describe the number of TSS (after proper pairing and deduplication) aligning to known regions in the genome.
-
promoter: Promoter regions.
-
exon: Known exons.
-
intron: Know introns (that is: the TSS matches a transcript but none of its exons).
-
unknown: None of the above; basically intergenic.
-
other: Normally there should not be anything in this category since unknown should catch all intergenic TSS. But sometimes there is a misdesign, for instance in the example data here, the annotation file contained one more category, "boundary", which was not handled correctly by smallCAGEqc.
The annotation is hierarchical (promoters have priority on exons, etc.), so the sum of the annotation columns above should be be equal to the counts column.
Different types of scopes
Step-by-step extraction
Shows how many pairs are removed by the extraction, cleaning, mapping (proper pairs) and transcript counting steps described above.
-
Extraction: The total number of pairs where a tag could not be extracted (extracted - cleaned).
-
Cleaning: The total number of pairs where a tag was discarded because it matched a reference or artefact sequence, or because it had low complexity (tagdust + rdna + spikes, or cleaned - mapped).
-
Mapping: The number of non-mapped pairs (mapped - properpairs).
-
Deduplication: The number of non-properly mapped pairs (properpairs - counts).
-
Counts: The number of molecule counts.
plotAnnot(libs, "steps", "steps")
QC report
Pairs are categorised as tag dust, rDNA, spikes, unmapped, non-proper, duplicates and counts, and normalised by the total number of extracted pairs. Non-extracted pairs are ignored.
Compared to "steps", this scope gives more details on the sequences removed at the TagDust and mapping stages of the processing pipeline.
-
Tag_dust, rDNA, Spikes: same numbers as in the tagdust, rdna and spikes columns of the metadata table.
-
Unmapped: The number of pairs that could not be mapped.
-
Non_proper: The number of pairs that did not have a proper alignment.
-
Duplicates: The number of pairs that do not add a molecule count.
-
Counts: same as in "steps".
plotAnnot(libs, "qc", "qc")
Annotation of the transcript or tag counts
The unique molecule counts are grouped in annotation categories ("promoter", "exon", "intron" and "intergenic"), as described above.
plotAnnot(libs[libs$counts > 0,], "counts", "counts")
Annotation of the mapped reads
Same as "counts", with the addition of duplicates and non-proper pairs. Therefore the plot represents all the mapped data.
plotAnnot(libs, "mapped", "mapped")
QC including annotations
Pairs are categorised by extraction step and genome annotation.
plotAnnot(libs, "all", "all")
Annotation, normalised by mapped reads
Same as all except that normalisation is relative to the number of mapped reads
plotAnnot(libs, "annotation", "annotation")
Contents of the libs table
libs
## samplename sampleid total extracted cleaned tagdust rdna spikes
## A01 A01 1 57836 44740 33456 11244 40 0
## A02 A02 2 56608 42798 31358 11404 36 0
## A03 A03 3 79068 60769 49450 11283 36 0
## A04 A04 4 51895 37394 26998 10356 40 0
## A05 A05 5 62074 45786 34516 11239 31 0
## A06 A06 6 44003 29504 21978 7471 55 0
## A07 A07 7 60988 42773 28707 14026 40 0
## A08 A08 8 32950 23815 17276 6508 31 0
## A09 A09 9 28039 21889 15656 6163 70 0
## A10 A10 10 33938 24986 18511 6455 20 0
## A11 A11 11 31996 24512 16077 8352 83 0
## A12 A12 12 31146 24500 16029 8435 36 0
## B01 B01 13 113516 79890 47354 6246 26290 0
## B02 B02 14 72654 50406 31768 4061 14577 0
## B03 B03 15 106809 62736 50864 6573 5299 0
## B04 B04 16 80569 47843 34153 6099 7591 0
## B05 B05 17 107056 65211 48808 6118 10285 0
## B06 B06 18 79748 43397 30860 4525 8012 0
## B07 B07 19 110920 65635 51751 4582 9302 0
## B08 B08 20 66320 45432 28835 6448 10149 0
## B09 B09 21 95686 62955 40331 4706 17918 0
## B10 B10 22 55199 33872 18625 5643 9604 0
## B11 B11 23 48259 30849 21371 4268 5210 0
## B12 B12 24 72900 46406 26727 4635 15044 0
## C01 C01 25 149338 89401 49290 7319 32792 0
## C02 C02 26 138463 88758 63852 2770 22136 0
## C03 C03 27 129733 84172 49076 4081 31015 0
## C04 C04 28 110834 65837 49627 3515 12695 0
## C05 C05 29 143846 78132 53696 4636 19800 0
## C06 C06 30 109061 68825 38230 5636 24959 0
## C07 C07 31 119133 75078 44183 3683 27212 0
## C08 C08 32 78937 50912 33410 3141 14361 0
## C09 C09 33 92263 57695 35157 4207 18331 0
## C10 C10 34 104621 64239 47782 3627 12830 0
## C11 C11 35 77071 43272 31482 2827 8963 0
## C12 C12 36 75814 44190 34379 2762 7049 0
## D01 D01 37 211918 108057 93175 687 14195 0
## D02 D02 38 126215 72882 61995 446 10441 0
## D03 D03 39 141855 72767 59564 392 12811 0
## D04 D04 40 176145 89332 79117 443 9772 0
## D05 D05 41 175940 86247 74584 587 11076 0
## D06 D06 42 121366 62256 53868 519 7868 1
## D07 D07 43 121058 61880 51964 503 9413 0
## D08 D08 44 72706 36161 29710 397 6054 0
## D09 D09 45 97847 42801 33270 371 9160 0
## D10 D10 46 100807 54161 46082 400 7679 0
## D11 D11 47 108622 53295 47374 470 5450 1
## D12 D12 48 128301 62093 54183 339 7571 0
## E01 E01 49 198156 114073 101593 262 12215 3
## E02 E02 50 110978 56915 50023 194 6698 0
## E03 E03 51 115523 59100 52904 219 5977 0
## E04 E04 52 64343 32652 29219 63 3370 0
## E05 E05 53 133978 64977 58020 281 6676 0
## E06 E06 54 110519 54552 48413 208 5930 1
## E07 E07 55 102993 52575 46403 215 5957 0
## E08 E08 56 88876 42892 39408 200 3282 2
## E09 E09 57 84478 36919 33088 145 3685 1
## E10 E10 58 98540 47225 41223 425 5577 0
## E11 E11 59 94995 48522 42903 193 5425 1
## E12 E12 60 59296 34992 31704 131 3157 0
## F01 F01 61 133894 69445 64738 179 4528 0
## F02 F02 62 104592 52786 49382 143 3260 1
## F03 F03 63 105865 56012 53310 194 2508 0
## F04 F04 64 151032 70854 67432 160 3262 0
## F05 F05 65 133736 62248 58816 203 3229 0
## F06 F06 66 112267 49548 47160 88 2298 2
## F07 F07 67 120527 56568 52913 192 3463 0
## F08 F08 68 81028 36749 34530 155 2064 0
## F09 F09 69 82247 37776 35593 208 1975 0
## F10 F10 70 116168 53753 50827 170 2755 1
## F11 F11 71 85752 41126 39325 168 1633 0
## F12 F12 72 96754 40894 39065 159 1670 0
## G01 G01 73 157245 77357 73610 185 3560 2
## G02 G02 74 140353 64494 61409 162 2923 0
## G03 G03 75 106273 48053 45657 214 2182 0
## G04 G04 76 161767 70158 67226 196 2736 0
## G05 G05 77 111602 48539 46504 151 1883 1
## G06 G06 78 145265 61302 58751 155 2396 0
## G07 G07 79 170602 68849 66149 272 2428 0
## G08 G08 80 85777 36517 34632 149 1736 0
## G09 G09 81 87382 34965 33038 171 1755 1
## G10 G10 82 80439 29017 28083 183 751 0
## G11 G11 83 76145 32785 31503 128 1153 1
## G12 G12 84 91108 35631 33763 169 1699 0
## H01 H01 85 167121 75412 72015 252 3145 0
## H02 H02 86 134912 59559 57087 148 2324 0
## H03 H03 87 98710 44567 42472 241 1854 0
## H04 H04 88 144495 58339 56288 204 1847 0
## H05 H05 89 129765 43742 41949 336 1457 0
## H06 H06 90 113057 42409 39991 139 2279 0
## H07 H07 91 176644 66278 63319 240 2719 0
## H08 H08 92 98958 34662 33525 196 941 0
## H09 H09 93 83042 29701 28537 171 993 0
## H10 H10 94 66452 20773 19790 81 902 0
## H11 H11 95 89280 27906 26841 166 899 0
## H12 H12 96 83539 28756 27666 148 942 0
## mapped properpairs counts group group_alpha row col Concentration
## A01 16191 161 128 0 0.000 1 A 0.162
## A02 15558 166 123 0 0.000 2 A 0.176
## A03 21330 211 159 0 0.000 3 A 0.162
## A04 11657 226 164 0 0.000 4 A 0.137
## A05 18286 291 215 0 0.000 5 A 0.152
## A06 10913 149 111 0 0.000 6 A 0.167
## A07 10873 0 0 0 0.000 7 A 0.177
## A08 8403 126 105 0 0.000 8 A 0.184
## A09 6973 135 98 0 0.000 9 A 0.208
## A10 9937 120 109 0 0.000 10 A 0.153
## A11 7830 208 126 0 0.000 11 A 0.161
## A12 7225 129 102 0 0.000 12 A 0.155
## B01 37640 22667 14343 5 0.005 1 B 0.156
## B02 24362 13744 7537 5 0.005 2 B 0.197
## B03 41386 17864 12282 5 0.005 3 B 0.203
## B04 26392 17496 11951 5 0.005 4 B 0.160
## B05 42219 23383 14708 5 0.005 5 B 0.154
## B06 26235 16390 9672 5 0.005 6 B 0.186
## B07 45950 27813 14672 5 0.005 7 B 0.243
## B08 23143 13753 8318 5 0.005 8 B 0.065
## B09 35094 20483 11170 5 0.005 9 B 0.230
## B10 13506 6561 3603 5 0.005 10 B 0.145
## B11 15098 7019 4573 5 0.005 11 B 0.145
## B12 21986 9790 5586 5 0.005 12 B 0.190
## C01 41268 27344 15537 10 0.010 1 C 0.247
## C02 59641 43036 29995 10 0.010 2 C 0.348
## C03 43278 34189 22366 10 0.010 3 C 0.235
## C04 45103 33171 19651 10 0.010 4 C 0.217
## C05 49398 30795 20012 10 0.010 5 C 0.267
## C06 34091 24496 18016 10 0.010 6 C 0.235
## C07 40045 29773 21171 10 0.010 7 C 0.155
## C08 29481 21380 14386 10 0.010 8 C 0.090
## C09 31130 22610 15230 10 0.010 9 C 0.276
## C10 42111 30183 20526 10 0.010 10 C 0.320
## C11 27613 18027 13697 10 0.010 11 C 0.223
## C12 30804 20590 13729 10 0.010 12 C 0.297
## D01 89865 65730 52248 50 0.050 1 D 0.530
## D02 60842 45193 34407 50 0.050 2 D 0.542
## D03 58729 47380 36083 50 0.050 3 D 0.620
## D04 77923 60089 44735 50 0.050 4 D 0.527
## D05 72447 56669 43199 50 0.050 5 D 0.497
## D06 52333 39002 31387 50 0.050 6 D 0.568
## D07 50824 39326 31103 50 0.050 7 D 0.771
## D08 28976 22389 18234 50 0.050 8 D 0.690
## D09 32704 24638 19555 50 0.050 9 D 0.616
## D10 44784 34443 27639 50 0.050 10 D 0.478
## D11 46716 35769 27793 50 0.050 11 D 0.604
## D12 53167 41331 33085 50 0.050 12 D 0.636
## E01 99997 79165 62741 100 0.100 1 E 0.472
## E02 48990 37058 30889 100 0.100 2 E 0.616
## E03 51701 41228 33789 100 0.100 3 E 0.633
## E04 28879 20711 17324 100 0.100 4 E 0.577
## E05 57053 44186 36254 100 0.100 5 E 0.523
## E06 47367 34363 28622 100 0.100 6 E 0.669
## E07 45657 34766 28742 100 0.100 7 E 0.802
## E08 38534 28422 23454 100 0.100 8 E 0.724
## E09 32387 23970 20526 100 0.100 9 E 0.606
## E10 39997 30301 27506 100 0.100 10 E 0.451
## E11 42451 32153 26738 100 0.100 11 E 0.614
## E12 31410 24025 20323 100 0.100 12 E 0.668
## F01 63961 49002 41263 500 0.500 1 F 0.974
## F02 48692 38696 32393 500 0.500 2 F 0.718
## F03 52663 40504 34118 500 0.500 3 F 0.723
## F04 66550 51626 43342 500 0.500 4 F 0.719
## F05 57743 43906 37310 500 0.500 5 F 0.720
## F06 46529 36544 31401 500 0.500 6 F 0.903
## F07 52396 40338 33918 500 0.500 7 F 0.887
## F08 34156 25786 22086 500 0.500 8 F 1.016
## F09 35174 26843 22878 500 0.500 9 F 1.009
## F10 50011 38554 32330 500 0.500 10 F 0.754
## F11 38810 29784 25397 500 0.500 11 F 0.871
## F12 38666 29332 25302 500 0.500 12 F 0.677
## G01 72874 56189 46184 1000 1.000 1 G 1.053
## G02 60664 45441 37084 1000 1.000 2 G 0.929
## G03 45000 33837 28132 1000 1.000 3 G 0.908
## G04 66289 51171 42594 1000 1.000 4 G 0.883
## G05 45715 35589 29503 1000 1.000 5 G 0.942
## G06 58119 43708 36940 1000 1.000 6 G 1.056
## G07 64834 47451 39214 1000 1.000 7 G 1.178
## G08 34114 24866 21295 1000 1.000 8 G 1.067
## G09 32645 23779 20003 1000 1.000 9 G 1.108
## G10 27695 20601 19151 1000 1.000 10 G 0.960
## G11 31184 24414 21011 1000 1.000 11 G 1.150
## G12 33260 25400 21678 1000 1.000 12 G 0.872
## H01 71031 53719 42839 2000 2.000 1 H 1.678
## H02 56441 43344 34846 2000 2.000 2 H 1.278
## H03 41591 31472 25730 2000 2.000 3 H 1.588
## H04 55498 43738 35853 2000 2.000 4 H 1.439
## H05 41274 31941 29084 2000 2.000 5 H 1.559
## H06 39554 31613 26223 2000 2.000 6 H 1.834
## H07 62372 45835 36225 2000 2.000 7 H 1.901
## H08 33016 25111 21283 2000 2.000 8 H 1.695
## H09 28126 20602 17633 2000 2.000 9 H 1.236
## H10 19449 14311 12514 2000 2.000 10 H 1.529
## H11 26455 20579 17642 2000 2.000 11 H 1.421
## H12 27106 21307 18492 2000 2.000 12 H 1.525
## Run l1 r100l1 exon intron other promoter unknown genes
## A01 1772-087-069 40 35.00393 2 42 0 10 74 12
## A02 1772-087-069 39 34.53797 0 38 0 9 76 10
## A03 1772-087-069 49 38.12546 7 36 0 12 104 16
## A04 1772-087-069 50 37.21116 0 46 0 7 111 15
## A05 1772-087-069 53 35.38931 6 49 0 31 129 20
## A06 1772-087-069 38 35.65686 1 35 0 9 66 11
## A07 1772-087-069 0 0.00000 0 0 0 0 0 0
## A08 1772-087-069 37 35.94311 2 24 0 19 60 13
## A09 1772-087-069 30 30.00000 2 16 0 3 77 9
## A10 1772-087-069 35 33.54695 2 21 0 12 74 8
## A11 1772-087-069 62 53.58818 17 21 0 16 72 22
## A12 1772-087-069 37 36.62609 1 30 0 2 69 10
## B01 1772-087-069 106 14.64366 6204 335 0 1938 5866 38
## B02 1772-087-069 290 19.19440 1926 419 0 4040 1152 80
## B03 1772-087-069 142 17.20786 179 261 0 6122 5720 30
## B04 1772-087-069 154 18.44604 1834 2255 0 4921 2941 51
## B05 1772-087-069 134 16.75237 132 786 0 2388 11402 31
## B06 1772-087-069 159 19.54335 365 2462 0 1466 5379 43
## B07 1772-087-069 211 18.26080 3529 636 0 2961 7546 53
## B08 1772-087-069 152 19.59785 17 2366 0 2154 3781 39
## B09 1772-087-069 344 28.23019 14 1154 0 1840 8162 40
## B10 1772-087-069 124 21.74362 66 1213 0 785 1539 37
## B11 1772-087-069 116 13.26322 1344 64 0 389 2776 24
## B12 1772-087-069 162 20.94065 64 1214 0 1563 2745 42
## C01 1772-087-069 242 25.48931 160 3797 0 2821 8759 61
## C02 1772-087-069 402 32.73442 971 7466 0 10701 10857 84
## C03 1772-087-069 305 27.92000 4783 6179 0 3044 8360 76
## C04 1772-087-069 370 31.87616 1798 1200 0 3225 13428 81
## C05 1772-087-069 440 31.36962 1199 5118 0 4552 9143 116
## C06 1772-087-069 212 22.82430 1817 579 0 7720 7900 59
## C07 1772-087-069 360 38.94175 2403 1797 1 5564 11406 93
## C08 1772-087-069 280 32.94986 2075 4031 3 3589 4688 70
## C09 1772-087-069 276 23.03263 293 3485 0 2464 8988 81
## C10 1772-087-069 417 45.88426 3744 5515 0 3529 7738 138
## C11 1772-087-069 241 27.15281 2437 1929 0 2658 6673 59
## C12 1772-087-069 293 28.72867 1261 3338 0 1090 8040 80
## D01 1772-087-069 1448 73.93816 6003 9940 0 9260 27045 348
## D02 1772-087-069 1405 77.98528 3542 8960 0 5350 16555 340
## D03 1772-087-069 1379 74.17269 2642 9327 0 4804 19310 300
## D04 1772-087-069 1581 76.47927 4336 9913 0 7374 23112 366
## D05 1772-087-069 1869 79.00155 2869 11857 0 4877 23596 394
## D06 1772-087-069 1715 78.34378 1972 7444 1 4598 17372 399
## D07 1772-087-069 1198 72.20326 3211 6987 0 5560 15345 296
## D08 1772-087-069 1002 72.18696 2923 4015 0 3575 7721 260
## D09 1772-087-069 1005 72.88108 2479 4706 0 2412 9958 270
## D10 1772-087-069 1507 78.98770 2867 6133 0 3407 15232 393
## D11 1772-087-069 1379 77.20211 2263 6242 1 3720 15567 337
## D12 1772-087-069 1392 77.06525 3876 8104 0 3738 17367 339
## E01 1772-087-069 2265 85.16074 5622 15233 0 7352 34534 556
## E02 1772-087-069 1900 85.41793 2566 7968 0 4010 16345 458
## E03 1772-087-069 1842 84.26035 3321 8877 0 4517 17073 466
## E04 1772-087-069 1658 85.84360 1608 4630 0 1513 9573 449
## E05 1772-087-069 2378 87.09019 3630 9858 0 3804 18962 559
## E06 1772-087-069 2138 87.99389 1837 5630 35 3990 17130 541
## E07 1772-087-069 1924 86.41941 2197 7446 0 3399 15700 497
## E08 1772-087-069 1765 86.77928 2110 5009 0 2402 13933 472
## E09 1772-087-069 1723 87.35975 2255 4181 2 2895 11193 483
## E10 1772-087-069 1793 85.70211 3102 6129 0 4647 13628 501
## E11 1772-087-069 1925 86.98539 2419 6827 1 3573 13918 507
## E12 1772-087-069 1814 87.78132 1325 4795 5 2504 11694 481
## F01 1772-087-069 3635 92.62051 4607 9108 4 3963 23581 917
## F02 1772-087-069 3358 92.82644 2575 8424 0 2852 18542 817
## F03 1772-087-069 3563 93.57936 3014 7998 0 3717 19389 854
## F04 1772-087-069 4136 93.90090 3620 9944 0 4850 24928 982
## F05 1772-087-069 3837 93.98819 3379 8444 1 4408 21078 930
## F06 1772-087-069 3741 93.91198 2160 7017 62 3832 18330 888
## F07 1772-087-069 3819 94.19979 3466 8135 0 3976 18341 951
## F08 1772-087-069 3155 94.12737 1746 5710 0 3014 11616 842
## F09 1772-087-069 3691 94.74871 2216 5101 23 2702 12836 967
## F10 1772-087-069 3615 92.98439 2627 7025 1 2741 19936 816
## F11 1772-087-069 3532 93.98666 1875 6082 0 2950 14490 932
## F12 1772-087-069 3669 94.64871 2066 6055 0 2218 14963 962
## G01 1772-087-069 4439 94.46853 4186 10762 39 6198 24999 1038
## G02 1772-087-069 4053 92.75496 3855 8373 0 3806 21050 949
## G03 1772-087-069 3752 93.66966 2697 7029 2 2832 15572 903
## G04 1772-087-069 3900 92.09875 4283 9929 0 4208 24174 850
## G05 1772-087-069 3356 92.67858 2740 6714 0 2979 17070 775
## G06 1772-087-069 3873 92.82608 3718 9021 0 4142 20059 914
## G07 1772-087-069 5138 94.78783 3631 9264 2 5200 21117 1242
## G08 1772-087-069 3977 94.43834 2051 5135 0 3144 10965 1080
## G09 1772-087-069 3806 95.08377 1742 4376 0 2667 11218 1024
## G10 1772-087-069 2642 92.13822 1432 4437 1 1757 11524 636
## G11 1772-087-069 3136 93.63214 1756 4911 0 2883 11461 800
## G12 1772-087-069 3411 94.58613 1795 4978 3 2374 12528 869
## H01 1772-087-069 4296 92.15265 4700 9467 7 4900 23765 980
## H02 1772-087-069 3697 93.16116 3503 8810 119 4394 18020 863
## H03 1772-087-069 3260 92.42869 2731 5836 0 2818 14345 802
## H04 1772-087-069 3112 90.11942 3835 7867 1 4015 20135 684
## H05 1772-087-069 2847 88.82836 3141 5493 1 3349 17100 677
## H06 1772-087-069 2671 85.46402 3499 5371 1 2258 15094 601
## H07 1772-087-069 4125 89.92747 4114 7256 0 3854 21001 934
## H08 1772-087-069 3086 92.93838 2827 5158 24 2465 10809 844
## H09 1772-087-069 3581 93.04251 2007 3820 0 2580 9226 986
## H10 1772-087-069 2565 93.39395 1287 3116 0 1515 6596 700
## H11 1772-087-069 2491 90.60411 1498 3957 0 2038 10149 595
## H12 1772-087-069 2738 91.97103 2105 4229 0 1751 10407 637
R session info
sessionInfo()
## R version 3.3.1 (2016-06-21)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Debian GNU/Linux 8 (jessie)
##
## locale:
## [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C
## [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.utf8
## [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.utf8
## [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] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] smallCAGEqc_0.12.2.99999 magrittr_1.5
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.2 knitr_1.13 munsell_0.4.2
## [4] lattice_0.20-29 colorspace_1.2-6 stringr_1.0.0
## [7] plyr_1.8.3 tools_3.3.1 grid_3.3.1
## [10] gtable_0.1.2 vegan_2.0-10 lambda.r_1.1.7
## [13] futile.logger_1.4.1 htmltools_0.2.6 gtools_3.5.0
## [16] yaml_2.1.13 digest_0.6.8 permute_0.8-3
## [19] ggplot2_2.1.0 formatR_1.4 futile.options_1.0.0
## [22] VennDiagram_1.6.16 evaluate_0.8 rmarkdown_0.9.6
## [25] labeling_0.3 gdata_2.17.0 stringi_1.0-1
## [28] scales_0.4.0 reshape_0.8.5
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