feature.matrix

Data Sets.

Bundled with openPrimeR · exported, loads via data()

Class

data.frame

Dimensions

908 × 32

Missing

53

Format

rda · xz

version 2 · 43 KB

File

data/RefCoverage.rda

Fingerprint

f9bbbf7e

Format documented

Yes

Source

Source not stated

About this object

Equal-length columns presented as a table, R's standard rectangular format. R object catalogue

Declared attributes

Row names

Yes

Columns

Column

Type

Distinct

Missing

Summary

Primer

factor

20

0

Tiller_5'LVH147Tiller_5'LVH347Tiller_5'LVH4_647Tiller_5'LVH547Opt5_147Opt5_1047+14 more

Levels

20

Used

20

Rows per level

Tiller_5'LVH147Tiller_5'LVH347Tiller_5'LVH4_647Tiller_5'LVH547Opt5_147Opt5_1047Opt5_1347Opt5_1447Opt5_1547Opt5_247Opt5_347Opt5_447Opt5_547Opt5_647Opt5_747Opt5_847Opt5_947Opt5_1645Opt5_1239Opt5_1125

Template

factor

47

0

IGHV1-220IGHV1-2420IGHV1-320IGHV1-4520IGHV1-4620IGHV2-2620+41 more

Levels

47

Used

47

Rows per level

IGHV1-220IGHV1-2420IGHV1-320IGHV1-4520IGHV1-4620IGHV2-2620IGHV2-520IGHV3-3020IGHV3-30-320IGHV3-3320IGHV3-64D20IGHV4-2820IGHV4-30-220IGHV4-3120IGHV4-3420IGHV4-38-220IGHV4-5920IGHV4-6120IGHV6-120IGHV1-1819IGHV1-5819IGHV1-6919IGHV1-69-219IGHV1-819IGHV2-7019IGHV3-1119IGHV3-1519IGHV3-2119IGHV3-4319IGHV3-4819IGHV3-4919IGHV3-5319IGHV3-6619IGHV3-719IGHV3-7219IGHV3-7319IGHV3-7419IGHV3-919IGHV4-3919IGHV4-419IGHV5-10-119IGHV5-5119IGHV7-4-119IGHV3-1318IGHV3-2018IGHV3-2318IGHV3-6418

Group

factor

47

0

IGHV1-220IGHV1-2420IGHV1-320IGHV1-4520IGHV1-4620IGHV2-2620+41 more

Levels

47

Used

47

Rows per level

IGHV1-220IGHV1-2420IGHV1-320IGHV1-4520IGHV1-4620IGHV2-2620IGHV2-520IGHV3-3020IGHV3-30-320IGHV3-3320IGHV3-64D20IGHV4-2820IGHV4-30-220IGHV4-3120IGHV4-3420IGHV4-38-220IGHV4-5920IGHV4-6120IGHV6-120IGHV1-1819IGHV1-5819IGHV1-6919IGHV1-69-219IGHV1-819IGHV2-7019IGHV3-1119IGHV3-1519IGHV3-2119IGHV3-4319IGHV3-4819IGHV3-4919IGHV3-5319IGHV3-6619IGHV3-719IGHV3-7219IGHV3-7319IGHV3-7419IGHV3-919IGHV4-3919IGHV4-419IGHV5-10-119IGHV5-5119IGHV7-4-119IGHV3-1318IGHV3-2018IGHV3-2318IGHV3-6418

Number_of_mismatches

integer

13

0

0 – 12mean 7.691

Min.

0

1st Qu.

6

Median

9

Mean

7.6905

3rd Qu.

10

Max.

12

Std. dev

3.7186

Skewness

-0.9017

Kurtosis

-0.5325

Zeros

53

primer_efficiency

numeric

169

0

0 – 1mean 0.1381

Min.

0

1st Qu.

0

Median

0

Mean

0.1381

3rd Qu.

0.0007

Max.

1

Std. dev

0.3203

Skewness

2.123

Kurtosis

2.745

Zeros

564

Outliers

2030 low · 203 high

annealing_DeltaG

numeric

407

0

-21.194 – -0.194mean -5.398

Min.

-21.194

1st Qu.

-6.4315

Median

-3.34

Mean

-5.398

3rd Qu.

-2.197

Max.

-0.194

Std. dev

4.579

Skewness

-1.381

Kurtosis

0.8932

Outliers

9090 low · 0 high

Position_3terminus

numeric

19

53

1 – 21mean 4.061

Min.

1

1st Qu.

1

Median

2

Mean

4.0608

3rd Qu.

6

Max.

21

Std. dev

4.0139

Skewness

1.434

Kurtosis

1.32

Outliers

220 low · 22 high

Longest gap

6

All_mismatches

character

508

0

1 – 33 characters

Worst_Case_MismatchLocal

character

68

0

1 – 23 characters

Primer_Sequence

character

20

0

18 – 27 characters

Terminal_Dinucleotide

character

6

0

2 characters

Mismatch_pos_1

numeric

2

0

0 – 1mean 0.326

Min.

0

1st Qu.

0

Median

0

Mean

0.326

3rd Qu.

1

Max.

1

Std. dev

0.469

Skewness

0.7412

Kurtosis

-1.452

Zeros

612

Mismatch_pos_2

numeric

2

0

0 – 1mean 0.2533

Min.

0

1st Qu.

0

Median

0

Mean

0.2533

3rd Qu.

1

Max.

1

Std. dev

0.4351

Skewness

1.133

Kurtosis

-0.718

Zeros

678

Mismatch_pos_3

numeric

2

0

0 – 1mean 0.3337

Min.

0

1st Qu.

0

Median

0

Mean

0.3337

3rd Qu.

1

Max.

1

Std. dev

0.4718

Skewness

0.7042

Kurtosis

-1.506

Zeros

605

Mismatch_pos_4

numeric

2

0

0 – 1mean 0.283

Min.

0

1st Qu.

0

Median

0

Mean

0.283

3rd Qu.

1

Max.

1

Std. dev

0.4507

Skewness

0.9617

Kurtosis

-1.076

Zeros

651

Mismatch_pos_5

numeric

2

0

0 – 1mean 0.3524

Min.

0

1st Qu.

0

Median

0

Mean

0.3524

3rd Qu.

1

Max.

1

Std. dev

0.478

Skewness

0.6168

Kurtosis

-1.621

Zeros

588

Mismatch_pos_6

numeric

2

0

0 – 1mean 0.3524

Min.

0

1st Qu.

0

Median

0

Mean

0.3524

3rd Qu.

1

Max.

1

Std. dev

0.478

Skewness

0.6168

Kurtosis

-1.621

Zeros

588

Hexamer_Mismatch_Count

numeric

7

0

0 – 6mean 1.901

Min.

0

1st Qu.

0

Median

2

Mean

1.9009

3rd Qu.

3

Max.

6

Std. dev

1.5486

Skewness

0.2134

Kurtosis

-1.115

Zeros

253

Experimental_Coverage

factor

2

0

Unamplified526Amplified382

primer_length_fw

integer

8

0

18 – 27mean 22.21

Min.

18

1st Qu.

21

Median

22

Mean

22.207

3rd Qu.

24

Max.

27

Std. dev

2.1019

Skewness

0.2748

Kurtosis

-0.2291

gc_clamp_fw

numeric

3

0

1 – 3mean 1.543

Min.

1

1st Qu.

1

Median

1

Mean

1.543

3rd Qu.

2

Max.

3

Std. dev

0.5934

Skewness

0.5775

Kurtosis

-0.6064

gc_ratio_fw

numeric

9

0

0.5 – 0.6667mean 0.589

Min.

0.5

1st Qu.

0.5714

Median

0.5909

Mean

0.589

3rd Qu.

0.6

Max.

0.6667

Std. dev

0.0411

Skewness

0.3127

Kurtosis

0.3714

Outliers

21170 low · 141 high

no_runs_fw

numeric

3

0

2 – 4mean 2.817

Min.

2

1st Qu.

2

Median

3

Mean

2.8172

3rd Qu.

3

Max.

4

Std. dev

0.7511

Skewness

0.3124

Kurtosis

-1.179

no_repeats_fw

numeric

3

0

1 – 3mean 1.584

Min.

1

1st Qu.

1

Median

2

Mean

1.5837

3rd Qu.

2

Max.

3

Std. dev

0.5852

Skewness

0.4147

Kurtosis

-0.7149

melting_temp

numeric

19

0

58.28 – 69mean 60.61

Min.

58.28

1st Qu.

59.05

Median

59.73

Mean

60.6127

3rd Qu.

60.96

Max.

69

Std. dev

2.8718

Skewness

2.071

Kurtosis

3.2

Outliers

940 low · 94 high

Self_Dimer_DeltaG

numeric

14

0

-2.255 – 0.407mean -1.263

Min.

-2.255

1st Qu.

-1.9638

Median

-1.308

Mean

-1.2626

3rd Qu.

-0.765

Max.

0.407

Std. dev

0.8458

Skewness

0.434

Kurtosis

-0.9892

Structure_deltaG_fw

numeric

9

0

-3.56 – 0mean -0.7211

Min.

-3.56

1st Qu.

-1.2925

Median

0

Mean

-0.7211

3rd Qu.

0

Max.

0

Std. dev

1.1511

Skewness

-1.363

Kurtosis

0.4043

Zeros

540

Outliers

4747 low · 0 high

primer_coverage

integer

4

0

25 – 47mean 45.95

Min.

25

1st Qu.

47

Median

47

Mean

45.9515

3rd Qu.

47

Max.

47

Std. dev

3.8975

Skewness

-4.504

Kurtosis

20.43

primer_specificity

numeric

5

0

0.3472 – 0.7966mean 0.5121

Min.

0.3472

1st Qu.

0.5

Median

0.5

Mean

0.5121

3rd Qu.

0.5

Max.

0.7966

Std. dev

0.0727

Skewness

2.773

Kurtosis

9.905

Run

character

2

0

14 characters

Position_3terminusLocal

numeric

7

0

0 – 6mean 3.544

Min.

0

1st Qu.

0

Median

5

Mean

3.5441

3rd Qu.

6

Max.

6

Std. dev

2.5014

Skewness

-0.4605

Kurtosis

-1.498

Zeros

253

Number_of_mismatches_hexamer

numeric

7

0

0 – 6mean 1.901

Min.

0

1st Qu.

0

Median

2

Mean

1.9009

3rd Qu.

3

Max.

6

Std. dev

1.5486

Skewness

0.2134

Kurtosis

-1.115

Zeros

253

Version history

Version	Released	Size	Change	Stored as	Confidence
3.23	2026-04-28	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.22	2025-10-29	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.21	2025-07-12	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.20	2024-10-29	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.19	2024-04-30	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.18	2023-10-24	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.17	2023-04-25	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.16	2022-11-01	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.15	2022-04-26	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.14	2021-10-26	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.13	2021-05-19	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.12	2020-11-14	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.11	2020-08-14	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.10	2019-10-29	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.9	2019-05-02	908 × 32	Unchanged	rda · xz version 2 · 43 KB	exact
3.8	2018-11-10	908 × 32	Data changed Dimensions 724 × 28 → 908 × 32 · Missing 0 → 53	rda · xz version 2 · 43 KB	exact
3.7	2018-04-30	724 × 28	Unchanged	rda · xz version 2 · 10 KB	exact
3.6	2018-03-22	724 × 28	–	rda · xz version 2 · 10 KB	exact

Dimensions is the row and column count. Missing is how many values were recorded as absent.