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cleavages_testthat

Bundled with GUIDEseq · provided in inst/extdata, read by path with system.file()

Class
list
Elements
7
Missing
0
Format
rds · gzip
version 3 · 680 KB
File
inst/extdata/cleavages_testthat.RDS
Fingerprint
32b0523c
About this object
A list with no shape constraintsRows of cells of visibly different widths, one below the next, with nothing lining them up and nothing in them, and under them a small block with a header band: an element of a list can be another structure. There is no common length, so there is no row count.list

R's general-purpose container. Elements can be any type and any size. R object catalogue

Structure
Distinct
7
Nesting depth
2
Element length
0 – 21
Total length
58
Nested rows
25,851
Nested columns
8
Nested schema
varies between elements
Elements
Element
Type
Distinct
Missing
Summary
cleavage.gr
GRanges
–
–
empty
unique.umi.plus.R2
list
8
0
nested·1,727 rows nested
Element length
1,727 – 1,727
Total length
13,816
Nested rows
1,727
What is inside it
Element
Type
Distinct
Missing
Summary
seqnames.last
factor
1
0
chr131,727+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr131,727
seqnames.first
factor
1
650
chr131,077+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr131,077
strand.last
factor
1
0
+1,727+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
+1,727
strand.first
factor
1
650
-1,077+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
-1,077
start.last
integer
967
0
19041139 – 115080749mean 6.068e+7
Min.
19041139
1st Qu.
38436035
Median
54002915
Mean
6.06843e+7
3rd Qu.
8.82114e+7
Max.
115080749
Std. dev
2.82859e+7
Skewness
0.3723
Kurtosis
-1.259
end.first
integer
757
650
19451291 – 115080905mean 5.997e+7
Min.
19451291
1st Qu.
39263015
Median
50251006
Mean
5.99669e+7
3rd Qu.
87153662
Max.
115080905
Std. dev
2.81744e+7
Skewness
0.4512
Kurtosis
-1.208
Longest gap
11
Leading
1
UMI
character
885
0
8 characters
n
integer
61
0
1 – 169mean 5.228
Min.
1
1st Qu.
1
Median
1
Mean
5.2276
3rd Qu.
5
Max.
169
Std. dev
11.9334
Skewness
7.202
Kurtosis
71.18
Outliers
1750 low · 175 high
unique.umi.minus.R2
list
8
0
nested·2,029 rows nested
Element length
2,029 – 2,029
Total length
16,232
Nested rows
2,029
What is inside it
Element
Type
Distinct
Missing
Summary
seqnames.last
factor
1
0
chr132,029+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr132,029
seqnames.first
factor
1
935
chr131,094+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr131,094
strand.last
factor
1
0
-2,029+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
-2,029
strand.first
factor
1
935
+1,094+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
+1,094
end.last
integer
1,013
0
19290710 – 115084370mean 6.35e+7
Min.
19290710
1st Qu.
38578902
Median
61122287
Mean
6.35011e+7
3rd Qu.
91361988
Max.
115084370
Std. dev
2.90698e+7
Skewness
0.2026
Kurtosis
-1.345
start.first
integer
746
935
19829456 – 115053178mean 6.298e+7
Min.
19829456
1st Qu.
38992087
Median
61122001
Mean
6.29808e+7
3rd Qu.
8.93028e+7
Max.
115053178
Std. dev
2.86651e+7
Skewness
0.217
Kurtosis
-1.358
Longest gap
10
UMI
character
908
0
8 characters
n
integer
59
0
1 – 240mean 4.444
Min.
1
1st Qu.
1
Median
2
Mean
4.4441
3rd Qu.
4
Max.
240
Std. dev
9.5072
Skewness
11.02
Kurtosis
210.7
Outliers
2340 low · 234 high
unique.umi.plus.R1
list
8
0
nested·44 rows nested
Element length
44 – 44
Total length
352
Nested rows
44
What is inside it
Element
Type
Distinct
Missing
Summary
seqnames.last
factor
1
42
chr132+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr132
seqnames.first
factor
1
0
chr1344+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr1344
strand.last
factor
1
42
+2+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
+2
strand.first
factor
1
0
-44+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
-44
start.first
integer
28
0
26444965 – 114821856mean 5.825e+7
Min.
26444965
1st Qu.
3.49511e+7
Median
5.02674e+7
Mean
5.82463e+7
3rd Qu.
8.16893e+7
Max.
114821856
Std. dev
2.81683e+7
Skewness
0.4669
Kurtosis
-1.261
start.last
integer
2
42
42609140 – 56195087mean 4.94e+7
Min.
42609140
1st Qu.
4.60056e+7
Median
4.94021e+7
Mean
4.94021e+7
3rd Qu.
5.27986e+7
Max.
56195087
Std. dev
9.60672e+6
Order
ascending
Longest gap
31
Leading
11
Trailing
31
UMI
character
41
0
8 characters
n
integer
10
0
1 – 17mean 3.318
Min.
1
1st Qu.
1
Median
1
Mean
3.3182
3rd Qu.
5
Max.
17
Std. dev
4.085
Skewness
1.824
Kurtosis
2.502
Outliers
40 low · 4 high
unique.umi.minus.R1
list
7
0
nested·41 rows nested
Element length
41 – 41
Total length
328
Nested rows
41
What is inside it
Element
Type
Distinct
Missing
Summary
seqnames.last
factor
0
41
25 levels
Levels
25
Unused
25
Rows per level, the 0 commonest of 25
seqnames.first
factor
1
0
chr1341+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr1341
strand.last
factor
0
41
3 levels
Levels
3
Unused
3
Rows per level, the 0 commonest of 3
strand.first
factor
1
0
+41+2 more
Levels
3
Used
1
Unused
2
Rows per level, the 1 commonest of 3
+41
end.first
integer
31
0
23766670 – 113406117mean 6.565e+7
Min.
23766670
1st Qu.
39262928
Median
58978672
Mean
6.56508e+7
3rd Qu.
93491789
Max.
113406117
Std. dev
2.87684e+7
Skewness
0.2229
Kurtosis
-1.467
end.last
integer
0
41
0 values
UMI
character
40
0
8 characters
n
integer
8
0
1 – 55mean 3.951
Min.
1
1st Qu.
1
Median
1
Mean
3.9512
3rd Qu.
2
Max.
55
Std. dev
9.3993
Skewness
4.359
Kurtosis
19.47
Outliers
70 low · 7 high
align.umi
list
21
0
nested·18,853 rows nested
Element length
18,853 – 18,853
Total length
395,913
Nested rows
18,853
What is inside it
Element
Type
Distinct
Missing
Summary
readName
character
18,431
0
47 – 49 characters
seqnames.first
factor
1
5,324
chr1313,529+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr1313,529
strand.first
factor
2
5,324
-8,266+5,263+1 more
Levels
3
Used
2
Unused
1
Rows per level, the 2 commonest of 3
-8,266+5,263
cigar.first
character
364
5,324
3 – 28 characters
qwidth.first
integer
110
5,324
18 – 150mean 127.6
Min.
18
1st Qu.
105
Median
147
Mean
127.558
3rd Qu.
150
Max.
150
Std. dev
31.0342
Skewness
-1.252
Kurtosis
0.6176
Outliers
163163 low · 0 high
Longest gap
7
start.first
integer
1,498
5,324
19451142 – 115080756mean 6.148e+7
Min.
19451142
1st Qu.
38436035
Median
55837751
Mean
6.14773e+7
3rd Qu.
90095091
Max.
115080756
Std. dev
2.87724e+7
Skewness
0.3296
Kurtosis
-1.338
Longest gap
7
end.first
integer
1,522
5,324
19451291 – 115080905mean 6.148e+7
Min.
19451291
1st Qu.
38436105
Median
55837857
Mean
6.14774e+7
3rd Qu.
90095236
Max.
115080905
Std. dev
2.87724e+7
Skewness
0.3296
Kurtosis
-1.338
Longest gap
7
width.first
integer
126
5,324
18 – 165mean 126.5
Min.
18
1st Qu.
103
Median
147
Mean
126.534
3rd Qu.
150
Max.
165
Std. dev
31.2226
Skewness
-1.193
Kurtosis
0.4679
Outliers
146146 low · 0 high
Longest gap
7
flag.first
integer
8
5,324
65 – 113mean 88.78
Min.
65
1st Qu.
83
Median
83
Mean
88.7827
3rd Qu.
99
Max.
113
Std. dev
7.9536
Skewness
0.401
Kurtosis
-1.513
Longest gap
7
mapq.first
integer
13
5,324
31 – 44mean 42.59
Min.
31
1st Qu.
42
Median
44
Mean
42.5948
3rd Qu.
44
Max.
44
Std. dev
2.4132
Skewness
-1.491
Kurtosis
0.9209
Outliers
1,3601360 low · 0 high
Longest gap
7
seqnames.last
factor
1
774
chr1318,079+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr1318,079
strand.last
factor
2
774
+9,045-9,034+1 more
Levels
3
Used
2
Unused
1
Rows per level, the 2 commonest of 3
+9,045-9,034
cigar.last
character
1,551
774
3 – 28 characters
qwidth.last
integer
36
774
39 – 150mean 124
Min.
39
1st Qu.
122
Median
122
Mean
124.023
3rd Qu.
128
Max.
150
Std. dev
4.8992
Skewness
-7.534
Kurtosis
127.9
Outliers
135105 low · 30 high
Longest gap
2
start.last
integer
3,082
774
19041139 – 115084341mean 6.211e+7
Min.
19041139
1st Qu.
38137739
Median
57201392
Mean
6.21077e+7
3rd Qu.
9.10591e+7
Max.
115084341
Std. dev
2.89025e+7
Skewness
0.2755
Kurtosis
-1.373
Longest gap
2
end.last
integer
2,944
774
19041173 – 115084370mean 6.211e+7
Min.
19041173
1st Qu.
38137857
Median
57201509
Mean
6.21078e+7
3rd Qu.
91059129
Max.
115084370
Std. dev
2.89025e+7
Skewness
0.2755
Kurtosis
-1.373
Longest gap
2
width.last
integer
107
774
24 – 130mean 109.1
Min.
24
1st Qu.
109
Median
118
Mean
109.056
3rd Qu.
122
Max.
130
Std. dev
23.2893
Skewness
-2.135
Kurtosis
3.871
Outliers
2,6802680 low · 0 high
Longest gap
2
flag.last
integer
8
774
129 – 177mean 154.5
Min.
129
1st Qu.
147
Median
147
Mean
154.47
3rd Qu.
163
Max.
177
Std. dev
8.9514
Skewness
-0.1649
Kurtosis
-0.6861
Longest gap
2
mapq.last
integer
10
774
32 – 44mean 42.86
Min.
32
1st Qu.
44
Median
44
Mean
42.8576
3rd Qu.
44
Max.
44
Std. dev
2.2526
Skewness
-1.768
Kurtosis
1.724
Longest gap
2
distance
integer
383
6,098
-14979778 – 564mean -1230
Min.
-14979778
1st Qu.
-103
Median
-78
Mean
-1230.11
3rd Qu.
-31
Max.
564
Std. dev
132637
Skewness
-112.9
Kurtosis
1.275e+4
Zeros
47
Outliers
7671 low · 766 high
Longest gap
8
UMI
character
1,229
0
8 characters
umi.count.summary
list
5
0
nested·3,157 rows nested
Element length
3,157 – 3,157
Total length
15,785
Nested rows
3,157
What is inside it
Element
Type
Distinct
Missing
Summary
seqnames
factor
1
0
chr133,157+24 more
Levels
25
Used
1
Unused
24
Rows per level, the 1 commonest of 25
chr133,157
strand
factor
2
0
-1,583+1,574+1 more
Levels
3
Used
2
Unused
1
Rows per level, the 2 commonest of 3
-1,583+1,574
start
integer
1,994
0
19041139 – 115084370mean 6.176e+7
Min.
19041139
1st Qu.
38106952
Median
57201392
Mean
6.17624e+7
3rd Qu.
88900995
Max.
115084370
Std. dev
2.87622e+7
Skewness
0.31
Kurtosis
-1.294
UMI
character
1,228
0
8 characters
n
integer
78
0
1 – 304mean 5.813
Min.
1
1st Qu.
1
Median
1
Mean
5.8134
3rd Qu.
6
Max.
304
Std. dev
13.0356
Skewness
8.457
Kurtosis
123.7
Outliers
3130 low · 313 high

The nested tables do not share one set of columns, so there is no single schema to show.

Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-04-287 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.222025-10-297 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.212025-04-157 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.202024-10-297 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.192024-04-307 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.182023-10-247 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.172023-04-257 elementsUnchangedrds · gzip
version 3 · 680 KB
exact
3.162022-11-017 elementsData changed
Class, Type, Missing and Distinct unchanged
rds · gzip
version 3 · 680 KB
exact
3.152022-04-267 elements–rds · gzip
version 3 · 680 KB
exact

Class is the chain of classes R records on the object, most specific first. The facts above give the short name for the same chain. 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.

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