methylBase.obj
Example methylBase object.
Bundled with methylKit · exported, loads via data()
Class
methylBase
Elements
16
Missing
0
Format
rda · gzip
version 3 · 81 KB
File
data/methylKit.RData
Fingerprint
f147a9eb
Structure
Distinct
15
Element length
963 – 963
Total length
15,408
Elements
Element
Type
Distinct
Missing
Summary
chr
character
1
0
5 characters
startinteger96309853296 – 19943695mean 1.446e+7
Min.
9853296
1st Qu.
1.01923e+7
Median
14370169
Mean
1.44643e+7
3rd Qu.
17214210
Max.
19943695
Std. dev
2.96539e+6
Skewness
-0.2519
Kurtosis
-1.072
Order
ascending
endinteger96309853296 – 19943695mean 1.446e+7
Min.
9853296
1st Qu.
1.01923e+7
Median
14370169
Mean
1.44643e+7
3rd Qu.
17214210
Max.
19943695
Std. dev
2.96539e+6
Skewness
-0.2519
Kurtosis
-1.072
Order
ascending
strand
character
2
0
1 characters
coverage1integer198010 – 818mean 81.76
Min.
10
1st Qu.
22
Median
68
Mean
81.7632
3rd Qu.
108
Max.
818
Std. dev
79.5632
Skewness
2.833
Kurtosis
13.74
Outliers
470 low · 47 high
numCs1integer17500 – 686mean 37.53
Min.
0
1st Qu.
0
Median
13
Mean
37.5327
3rd Qu.
41
Max.
686
Std. dev
67.0294
Skewness
3.703
Kurtosis
19.46
Zeros
285
Outliers
890 low · 89 high
numTs1integer16000 – 300mean 44.22
Min.
0
1st Qu.
3
Median
21
Mean
44.2181
3rd Qu.
80
Max.
300
Std. dev
49.4037
Skewness
1.074
Kurtosis
0.6261
Zeros
106
Outliers
30 low · 3 high
coverage2integer128010 – 630mean 48.16
Min.
10
1st Qu.
27
Median
37
Mean
48.1599
3rd Qu.
50
Max.
630
Std. dev
50.5352
Skewness
5.58
Kurtosis
41.88
Outliers
750 low · 75 high
numCs2integer11800 – 600mean 29.31
Min.
0
1st Qu.
0
Median
21
Mean
29.3063
3rd Qu.
37.5
Max.
600
Std. dev
47.6594
Skewness
5.605
Kurtosis
44.84
Zeros
284
Outliers
370 low · 37 high
numTs2integer8800 – 159mean 18.85
Min.
0
1st Qu.
2
Median
10
Mean
18.8474
3rd Qu.
30
Max.
159
Std. dev
22.0161
Skewness
1.943
Kurtosis
6.042
Zeros
88
Outliers
280 low · 28 high
coverage3integer140010 – 612mean 44.15
Min.
10
1st Qu.
21
Median
29
Mean
44.1526
3rd Qu.
49
Max.
612
Std. dev
48.3038
Skewness
4.879
Kurtosis
35.8
Outliers
770 low · 77 high
numCs3integer13100 – 608mean 27.5
Min.
0
1st Qu.
0
Median
16
Mean
27.4964
3rd Qu.
33
Max.
608
Std. dev
45.1849
Skewness
4.819
Kurtosis
39.69
Zeros
319
Outliers
660 low · 66 high
numTs3integer7900 – 158mean 16.65
Min.
0
1st Qu.
1
Median
10
Mean
16.6521
3rd Qu.
25
Max.
158
Std. dev
19.4345
Skewness
2.02
Kurtosis
6.742
Zeros
190
Outliers
350 low · 35 high
coverage4integer78010 – 395mean 23.12
Min.
10
1st Qu.
12.5
Median
16
Mean
23.1163
3rd Qu.
23
Max.
395
Std. dev
29.2051
Skewness
8.143
Kurtosis
84.71
Outliers
900 low · 90 high
numCs4integer7700 – 341mean 13.59
Min.
0
1st Qu.
0
Median
10
Mean
13.5919
3rd Qu.
17
Max.
341
Std. dev
25.8327
Skewness
7.572
Kurtosis
78.3
Zeros
330
Outliers
520 low · 52 high
numTs4integer4600 – 141mean 9.521
Min.
0
1st Qu.
1
Median
8
Mean
9.5213
3rd Qu.
14
Max.
141
Std. dev
12.0201
Skewness
4.911
Kurtosis
43.09
Zeros
211
Outliers
130 low · 13 high
Declared attributes
Other attributes
Read by name, kind and length, with the value where it is short enough to show. No rule here knows what any of them means.
| Attribute | Holds | Length | Value |
|---|---|---|---|
| .S3Class | character | 1 | data.frame |
| assembly | character | 1 | hg18 |
| context | character | 1 | CpG |
| coverage.index | numeric | 4 | 5, 8, 11, 14 |
| destranded | logical | 1 | FALSE |
| numCs.index | numeric | 4 | 6, 9, 12, 15 |
| numTs.index | numeric | 4 | 7, 10, 13, 16 |
| resolution | character | 1 | base |
| sample.ids | character | 4 | test1, test2, ctrl1, ctrl2 |
| treatment | numeric | 4 | 1, 1, 0, 0 |
Version history
| Version | Released | Rows × Cols | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.22 | 2025-10-29 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.21 | 2025-04-15 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.20 | 2025-02-28 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.19 | 2024-04-30 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.18 | 2023-10-24 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.17 | 2023-04-25 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.16 | 2022-11-01 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.15 | 2022-04-26 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.14 | 2021-10-26 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.13 | 2021-05-19 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.12 | 2021-01-28 | – | Unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.11 | 2020-05-20 | – | Data changed Class, Type, Missing and Distinct unchanged | rda · gzip version 3 · 81 KB | exact |
| 3.10 | 2019-10-29 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.9 | 2019-05-02 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.8 | 2018-12-11 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.7 | 2018-10-11 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.6 | 2018-01-22 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.5 | 2017-08-24 | – | Unchanged | rda · gzip version 2 · 89 KB | exact |
| 3.4 | 2016-10-17 | – | – | rda · gzip version 2 · 89 KB | exact |
Class is what R calls the object. Type is what the values in it are. Missing is how many values were recorded as absent. Distinct is how many different values were counted in the object.