association_file
Example of association file.
Bundled with ISAnalytics · exported, loads via data()
Class
data.table
data.table/data.frame
Dimensions
53 × 83
Missing
1,896
Format
rda · xz
version 3 · 4.2 KB
File
data/association_file.RData
Fingerprint
9bdaa42e
About this object
A data.frame with a key. The key is a sort order held with the table, and it is what makes joins and lookups fast, so it survives being saved and describes the file rather than a session. Loaded from an rda its internal self-reference is stale, so the first assignment by reference warns unless the package calls setalloccol() when it loads. R object catalogue
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 | |
|---|---|---|---|
| .internal.selfref | NULL | 0 |
Columns
Column
Type
Distinct
Missing
Summary
ProjectID
character
1
0
4 characters
FUSIONID
character
53
0
7 – 9 characters
PoolID
character
4
0
6 characters
TagSequence
character
53
0
8 – 9 characters
SubjectID
character
2
0
5 characters
VectorType
character
1
0
5 characters
VectorID
character
1
0
5 characters
ExperimentID
character
0
53
–
Tissue
character
2
0
2 characters
TimePoint
character
5
0
4 characters
DNAFragmentation
character
1
0
5 characters
PCRMethod
character
1
0
4 characters
TagIDextended
character
53
0
8 – 9 characters
Keywords
character
0
53
–
CellMarker
character
1
0
3 characters
TagID
character
53
0
9 – 10 characters
NGSProvider
character
0
53
–
NGSTechnology
character
1
0
5 characters
ConverrtedFilesDir
character
0
53
–
ConverrtedFilesName
character
0
53
–
SourceFileFolder
character
0
53
–
SourceFileNameR1
character
0
53
–
SourceFileNameR2
character
0
53
–
DNAnumber
character
20
0
8 – 9 characters
ReplicateNumberinteger301 – 3mean 2
Min.
1
1st Qu.
1
Median
2
Mean
2
3rd Qu.
3
Max.
3
Std. dev
0.8086
Skewness
3.435e-16
Kurtosis
-1.499
DNAextractionDateDate1202016-02-16 – 2017-05-24
Min.
2016-02-16
1st Qu.
2016-04-15
Median
2016-07-15
Mean
2016-08-10
3rd Qu.
2016-12-09
Max.
2017-05-24
DNAngUsednumeric20023.058 – 300.48mean 141.3
Min.
23.058
1st Qu.
45.15
Median
135.15
Mean
141.252
3rd Qu.
181.5
Max.
300.48
Std. dev
93.1899
Skewness
0.3519
Kurtosis
-0.9388
LinearPCRID
character
0
53
–
LinearPCRDate
Date
0
53
–
SonicationDateDate502016-11-02 – 2018-03-12
Min.
2016-11-02
1st Qu.
2016-11-02
Median
2017-04-19
Mean
2017-03-16
3rd Qu.
2017-05-03
Max.
2018-03-12
LigationDateDate502016-11-02 – 2018-03-12
Min.
2016-11-02
1st Qu.
2016-11-02
Median
2017-04-19
Mean
2017-03-16
3rd Qu.
2017-05-03
Max.
2018-03-12
1stExpoPCRID
character
53
0
7 – 9 characters
1stExpoPCRDateDate502016-11-02 – 2018-03-12
Min.
2016-11-02
1st Qu.
2016-11-02
Median
2017-04-20
Mean
2017-03-16
3rd Qu.
2017-05-04
Max.
2018-03-12
2ndExpoID
character
0
53
–
2ndExpoDate
Date
0
53
–
FusionPrimerPCRID
character
53
0
7 – 9 characters
FusionPrimerPCRDateDate502016-11-03 – 2018-03-12
Min.
2016-11-03
1st Qu.
2016-11-03
Median
2017-04-21
Mean
2017-03-17
3rd Qu.
2017-05-05
Max.
2018-03-12
PoolDateDate402016-11-07 – 2018-03-13
Min.
2016-11-07
1st Qu.
2016-11-07
Median
2017-05-17
Mean
2017-03-25
3rd Qu.
2017-05-17
Max.
2018-03-13
SequencingDateDate302016-11-15 – 2018-03-15
Min.
2016-11-15
1st Qu.
2016-11-15
Median
2017-06-23
Mean
2017-04-14
3rd Qu.
2017-06-23
Max.
2018-03-15
VCNnumeric1900.18 – 2.52mean 0.9642
Min.
0.18
1st Qu.
0.26
Median
0.77
Mean
0.9642
3rd Qu.
1.43
Max.
2.52
Std. dev
0.7967
Skewness
0.6819
Kurtosis
-1.041
Genome
character
1
0
4 characters
SequencingRoundinteger101 – 1mean 1
Min.
1
1st Qu.
1
Median
1
Mean
1
3rd Qu.
1
Max.
1
Std. dev
0
Order
constant
Genotype
character
0
53
–
TestGroup
character
0
53
–
MOI
character
0
53
–
Engraftment
numeric
0
53
0 values
Transduction
numeric
0
53
0 values
Notes
character
0
53
–
AddedField1
character
0
53
–
AddedField2
character
0
53
–
AddedField3
character
0
53
–
AddedField4
character
0
53
–
concatenatePoolIDSeqRun
character
4
0
8 characters
AddedField6_RelativeBloodPercentage
character
0
53
–
AddedField7_PurityTestFeasibility
numeric
0
53
0 values
AddedField8_FacsSeparationPurity
numeric
0
53
0 values
Kapanumeric6473.8202 – 57.1285mean 30.2
Min.
3.8202
1st Qu.
11.4378
Median
29.0545
Mean
30.2003
3rd Qu.
49.6977
Max.
57.1285
Std. dev
23.0383
Skewness
0.0329
Kurtosis
-2.126
Longest gap
26
Leading
26
Trailing
9
ulForPoolnumeric3471 – 3.9265mean 1.576
Min.
1
1st Qu.
1
Median
1
Mean
1.5758
3rd Qu.
1.3964
Max.
3.9265
Std. dev
1.1708
Skewness
1.269
Kurtosis
-0.2531
Outliers
10 low · 1 high
Longest gap
26
Leading
26
Trailing
9
CompleteAmplificationID
character
53
0
66 – 68 characters
UniqueID
character
53
0
22 characters
StudyTestID
character
0
53
–
StudyTestGroup
integer
0
53
0 values
MouseID
integer
0
53
0 values
Tigroup
character
0
53
–
Tisource
character
0
53
–
PathToFolderProjectID
character
1
0
5 characters
SamplesNameCheck
character
0
53
–
TimepointDays
character
5
0
4 characters
TimepointMonths
character
5
0
2 characters
TimepointYears
character
1
0
2 characters
ng DNA correctednumeric20023.06 – 300.48mean 141.3
Min.
23.06
1st Qu.
45.15
Median
135.15
Mean
141.252
3rd Qu.
181.5
Max.
300.48
Std. dev
93.1894
Skewness
0.3519
Kurtosis
-0.9388
RUN_NAME
character
4
0
13 characters
PHIX_MAPPINGinteger4018979629 – 51183662mean 3.382e+7
Min.
18979629
1st Qu.
18979629
Median
43586699
Mean
3.38221e+7
3rd Qu.
43586699
Max.
51183662
Std. dev
1.32164e+7
Skewness
-0.1614
Kurtosis
-1.858
PLASMID_MAPPED_BYPOOLinteger40392602 – 2256176mean 1.551e+6
Min.
392602
1st Qu.
1074651
Median
1074651
Mean
1.55078e+6
3rd Qu.
2256176
Max.
2256176
Std. dev
689915
Skewness
-0.1818
Kurtosis
-1.516
BARCODE_MUXinteger5307477 – 6120512mean 7.573e+5
Min.
7477
1st Qu.
346363
Median
484852
Mean
757265
3rd Qu.
660233
Max.
6120512
Std. dev
1.12506e+6
Skewness
3.542
Kurtosis
12.55
Outliers
50 low · 5 high
LTR_IDENTIFIEDinteger5307477 – 6120512mean 7.572e+5
Min.
7477
1st Qu.
346362
Median
484843
Mean
757206
3rd Qu.
660117
Max.
6120512
Std. dev
1.12506e+6
Skewness
3.542
Kurtosis
12.55
Outliers
50 low · 5 high
TRIMMING_FINAL_LTRLCinteger5307474 – 6104882mean 7.536e+5
Min.
7474
1st Qu.
342932
Median
480224
Mean
753568
3rd Qu.
654590
Max.
6104882
Std. dev
1.12149e+6
Skewness
3.542
Kurtosis
12.55
Outliers
50 low · 5 high
LV_MAPPEDinteger5303182 – 2926769mean 3.487e+5
Min.
3182
1st Qu.
153595
Median
211757
Mean
348665
3rd Qu.
303300
Max.
2926769
Std. dev
538064
Skewness
3.578
Kurtosis
12.75
Outliers
50 low · 5 high
BWA_MAPPED_OVERALLinteger5303944 – 2900368mean 3.642e+5
Min.
3944
1st Qu.
162504
Median
234853
Mean
364227
3rd Qu.
368752
Max.
2900368
Std. dev
534806
Skewness
3.458
Kurtosis
11.95
Outliers
40 low · 4 high
ISS_MAPPED_OVERALLinteger5302824 – 1966725mean 2.371e+5
Min.
2824
1st Qu.
92043
Median
149385
Mean
237097
3rd Qu.
221993
Max.
1966725
Std. dev
370638
Skewness
3.396
Kurtosis
11.26
Outliers
40 low · 4 high
RAW_READS
integer
0
53
0 values
QUALITY_PASSED
integer
0
53
0 values
ISS_MAPPED_PP
integer
0
53
0 values
Version history
| Version | Released | Rows × Cols | Change | Stored as | Confidence |
|---|---|---|---|---|---|
| 3.23 | 2026-04-28 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.22 | 2026-01-27 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.21 | 2025-04-15 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.20 | 2024-12-05 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.19 | 2024-04-30 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.18 | 2023-10-24 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.17 | 2023-07-24 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.16 | 2023-04-03 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.15 | 2022-05-23 | 53 × 83 | Unchanged | rda · xz version 3 · 4.2 KB | exact |
| 3.14 | 2022-01-13 | 53 × 83 | – | rda · xz version 3 · 4.2 KB | exact |