DEG_Methylation_Annotations

Output example from GMA function

Bundled with Moonlight2R · exported, loads via data()

Class

tibble

tbl_df/tbl/data.frame

Dimensions

3,435 × 35

Missing

96,815

Format

rda · gzip

version 3 · 159 KB

File

data/DEG_Methylation_Annotations.rda

Fingerprint

9b729e6b

Format documented

Yes

Source

Source not stated

About this object

A tibble: a data.frame that prints compactly, never converts strings to factors, never adds row names, and can hold list columns. R object catalogue

Columns

Column

Type

Distinct

Missing

Summary

Hugo_Symbol

character

3,390

2 – 12 characters

chromosome

character

3,362

4 – 5 characters

start

numeric

3,362

846055 – 246565425mean 7.157e+7

Min.

846055

1st Qu.

30911810

Median

47229803

Mean

7.15717e+7

3rd Qu.

127673363

Max.

246565425

Std. dev

5.96526e+7

Skewness

1.066

Kurtosis

0.698

Longest gap

3,362

Trailing

3,362

end

numeric

3,362

846056 – 246565426mean 7.157e+7

Min.

846056

1st Qu.

30911811

Median

47229804

Mean

7.15717e+7

3rd Qu.

127673364

Max.

246565426

Std. dev

5.96526e+7

Skewness

1.066

Kurtosis

0.698

Longest gap

3,362

Trailing

3,362

Probe

character

3,362

10 characters

State

character

3,362

4 – 5 characters

Prevalence of hypo (%)

numeric

3,362

0 – 100mean 20.55

Min.

1st Qu.

Median

Mean

20.5479

3rd Qu.

Max.

100

Std. dev

39.5345

Skewness

1.45

Kurtosis

0.1849

Zeros

Longest gap

3,362

Trailing

3,362

Prevalence of hyper (%)

numeric

3,362

0 – 100mean 70.27

Min.

1st Qu.

47.059

Median

100

Mean

70.2659

3rd Qu.

100

Max.

100

Std. dev

41.651

Skewness

-0.9108

Kurtosis

-0.9537

Zeros

Longest gap

3,362

Trailing

3,362

Comparators

character

3,362

14 – 15 characters

Raw.p

numeric

3,362

0.0017 – 0.038mean 0.0074

Min.

0.0017

1st Qu.

0.0035

Median

0.0035

Mean

0.0074

3rd Qu.

0.0084

Max.

0.038

Std. dev

0.0076

Skewness

2.142

Kurtosis

4.682

Outliers

140 low · 14 high

Longest gap

3,362

Trailing

3,362

Adjusted.p

numeric

3,362

0.0027 – 0.038mean 0.0079

Min.

0.0027

1st Qu.

0.0035

Median

0.0038

Mean

0.0079

3rd Qu.

0.0084

Max.

0.038

Std. dev

0.0075

Skewness

2.083

Kurtosis

4.488

Outliers

150 low · 15 high

Longest gap

3,362

Trailing

3,362

Probe_enhancer

character

3,435

–

Probe_in_enhancer

character

3,435

–

State_enhancer

character

3,435

–

Prevalence of hypo (%)_enhancer

numeric

3,435

0 values

Prevalence of hyper (%)_enhancer

numeric

3,435

0 values

Comparators_enhancer

character

3,435

–

Raw.p_enhancer

numeric

3,435

0 values

Adjusted.p_enhancer

numeric

3,435

0 values

logFC

numeric

3,390

-6.0865 – 10.5679mean 0.5692

Min.

-6.0865

1st Qu.

-1.4041

Median

1.1617

Mean

0.5692

3rd Qu.

1.9403

Max.

10.5679

Std. dev

2.3711

Skewness

0.106

Kurtosis

0.2657

Outliers

310 low · 31 high

logCPM

numeric

3,390

0.4169 – 12.8257mean 3.878

Min.

0.4169

1st Qu.

2.1565

Median

3.7435

Mean

3.8785

3rd Qu.

5.3511

Max.

12.8257

Std. dev

2.1373

Skewness

0.465

Kurtosis

-0.1771

Outliers

140 low · 14 high

numeric

3,390

8.173 – 2848.03mean 281.8

Min.

8.173

1st Qu.

97.0015

Median

187.561

Mean

281.805

3rd Qu.

367.798

Max.

2848.03

Std. dev

295.009

Skewness

2.776

Kurtosis

11.46

Outliers

1950 low · 195 high

PValue

numeric

3,355

0 – 0.0043mean 0

Min.

1st Qu.

5.6552e-82

Median

1.0831e-42

Mean

3rd Qu.

6.9377e-23

Max.

0.0043

Std. dev

0.0002

Skewness

19.48

Kurtosis

416.2

Zeros

Outliers

8390 low · 839 high

FDR

numeric

3,338

0 – 0.0054mean 0

Min.

1st Qu.

9.2239e-81

Median

7.0276e-42

Mean

3rd Qu.

2.2256e-22

Max.

0.0054

Std. dev

0.0002

Skewness

19.23

Kurtosis

405.6

Zeros

Outliers

8390 low · 839 high

Moonlight_gene_z_score

numeric

3,423

0.6931 – 3.7288mean 2.045

Min.

0.6931

1st Qu.

1.1233

Median

1.8419

Mean

2.0445

3rd Qu.

2.9065

Max.

3.7288

Std. dev

0.9908

Skewness

0.2672

Kurtosis

-1.495

Longest gap

3,269

Leading

Trailing

3,269

Moonlight_Oncogenic_Mediator

character

3,423

3 characters

promoter_start

numeric

3,411

841797 – 246565202mean 109488984

Min.

841797

1st Qu.

47228841

Median

1.27734e+8

Mean

109488984

3rd Qu.

141431249

Max.

246565202

Std. dev

7.17554e+7

Skewness

0.4159

Kurtosis

-0.6939

Longest gap

3,363

Trailing

3,363

promoter_end

numeric

3,411

847136 – 246565510mean 1.095e+8

Min.

847136

1st Qu.

47233139

Median

1.27735e+8

Mean

1.09491e+8

3rd Qu.

141431725

Max.

246565510

Std. dev

7.17544e+7

Skewness

0.4159

Kurtosis

-0.6939

Longest gap

3,363

Trailing

3,363

Probe_in_promoter

character

3,411

8 characters

NCG_driver

character

2,788

3 – 9 characters

NCG_cgc_annotation

character

3,308

3 – 21 characters

NCG_vogelstein_annotation

character

3,416

3 – 8 characters

NCG_saito_annotation

character

3,418

3 – 8 characters

NCG_pubmed_id

character

303

2,788

8 – 778 characters

NCG_cancer_type

character

158

2,918

8 – 389 characters

Version history

Version	Released	Size	Change	Stored as	Confidence
3.23	2026-06-30	3,435 × 35	Unchanged	rda · gzip version 3 · 159 KB	exact
3.22	2025-12-09	3,435 × 35	Unchanged	rda · gzip version 3 · 159 KB	exact
3.21	2025-10-10	3,435 × 35	Unchanged	rda · gzip version 3 · 159 KB	exact
3.20	2024-10-29	3,435 × 35	Unchanged	rda · gzip version 3 · 159 KB	exact
3.19	2024-04-30	3,435 × 35	–	rda · gzip version 3 · 159 KB	exact