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dataMAF

Mutation data from TCGA LUAD

Bundled with Moonlight2R · exported, loads via data()

Class
data.frame
Dimensions
500 × 141
Missing
34,108
Format
rda · gzip
version 3 · 191 KB
File
data/dataMAF.rda
Fingerprint
135956e7
Format documented
Yes
Source
Source not stated
About this object
A table with named columnsA bordered table: a header band ruled off from the body with an empty slot over each column where its name goes, and rows of cells under it that share every edge. Nothing is in any of them.

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

Columns
Column
Type
Distinct
Missing
Summary
X1
factor
274
0
17972726343639064756775+612 more
Levels
618
Used
274
Unused
344
Rows per level, the 50 commonest of 618
179727263436390647567751485153520252155235530653475383545154955561512641594219423842944296433743404344440045214526454641532533035636738839931023138316331713180318932853297330233093346335333663
Hugo_Symbol
character
467
0
2 – 11 characters
Entrez_Gene_Id
integer
463
0
0 – 100526835mean 4.831e+5
Min.
0
1st Qu.
5928
Median
29463
Mean
483125
3rd Qu.
98898.8
Max.
100526835
Std. dev
6.33496e+6
Skewness
15.66
Kurtosis
243.8
Zeros
5
Outliers
570 low · 57 high
Center
character
1
0
2 characters
NCBI_Build
character
1
0
6 characters
Chromosome
character
23
0
4 – 5 characters
Start_Position
integer
500
0
86289 – 248681752mean 8.096e+7
Min.
86289
1st Qu.
3.69074e+7
Median
64401061
Mean
8.09627e+7
3rd Qu.
1.21526e+8
Max.
248681752
Std. dev
5.75339e+7
Skewness
0.8255
Kurtosis
-0.0058
Outliers
10 low · 1 high
End_Position
integer
500
0
86289 – 248681752mean 8.096e+7
Min.
86289
1st Qu.
3.69074e+7
Median
64401061
Mean
8.09627e+7
3rd Qu.
1.21526e+8
Max.
248681752
Std. dev
5.75339e+7
Skewness
0.8255
Kurtosis
-0.0058
Outliers
10 low · 1 high
Strand
character
1
0
1 characters
Variant_Classification
character
13
0
3 – 22 characters
Variant_Type
character
3
0
3 characters
Reference_Allele
character
6
0
1 – 20 characters
Tumor_Seq_Allele1
character
6
0
1 – 20 characters
Tumor_Seq_Allele2
character
6
0
1 – 2 characters
dbSNP_RS
character
99
358
5 – 12 characters
dbSNP_Val_Status
character
0
500
–
Tumor_Sample_Barcode
character
274
0
28 characters
Matched_Norm_Sample_Barcode
character
258
0
28 characters
Match_Norm_Seq_Allele1
character
0
500
–
Match_Norm_Seq_Allele2
character
0
500
–
Tumor_Validation_Allele1
character
0
500
–
Tumor_Validation_Allele2
character
0
500
–
Match_Norm_Validation_Allele1
character
0
500
–
Match_Norm_Validation_Allele2
character
0
500
–
Verification_Status
character
0
500
–
Validation_Status
character
0
500
–
Mutation_Status
character
1
0
7 characters
Sequencing_Phase
character
0
500
–
Sequence_Source
character
0
500
–
Validation_Method
character
0
500
–
Score
character
0
500
–
BAM_File
character
0
500
–
Sequencer
character
0
500
–
Tumor_Sample_UUID
character
274
0
36 characters
Matched_Norm_Sample_UUID
character
258
0
36 characters
HGVSc
character
491
1
6 – 15 characters
HGVSp
character
472
26
7 – 19 characters
HGVSp_Short
character
482
15
5 – 14 characters
Transcript_ID
character
467
0
15 characters
Exon_Number
character
254
19
3 – 7 characters
t_depth
integer
209
0
9 – 846mean 113.4
Min.
9
1st Qu.
52
Median
86
Mean
113.364
3rd Qu.
138
Max.
846
Std. dev
99.344
Skewness
2.952
Kurtosis
13.69
Outliers
320 low · 32 high
t_ref_count
integer
190
0
2 – 766mean 88.75
Min.
2
1st Qu.
35
Median
66
Mean
88.754
3rd Qu.
111
Max.
766
Std. dev
88.3396
Skewness
3.262
Kurtosis
16.67
Outliers
350 low · 35 high
t_alt_count
integer
82
0
4 – 170mean 24.42
Min.
4
1st Qu.
10
Median
17
Mean
24.416
3rd Qu.
30
Max.
170
Std. dev
22.1182
Skewness
2.496
Kurtosis
8.543
Outliers
360 low · 36 high
n_depth
integer
212
0
10 – 896mean 114.5
Min.
10
1st Qu.
55
Median
88.5
Mean
114.544
3rd Qu.
138
Max.
896
Std. dev
98.1579
Skewness
2.846
Kurtosis
12.63
Outliers
330 low · 33 high
n_ref_count
character
0
500
–
n_alt_count
character
0
500
–
all_effects
character
500
0
71 – 4,053 characters
Allele
character
6
0
1 – 2 characters
Gene
character
467
0
15 characters
Feature
character
467
0
15 characters
Feature_type
character
1
0
10 characters
One_Consequence
character
13
0
9 – 34 characters
Consequence
character
16
0
9 – 40 characters
cDNA_position
character
481
19
4 – 15 characters
CDS_position
character
474
26
5 – 15 characters
Protein_position
character
474
26
5 – 14 characters
Amino_acids
character
145
26
1 – 9 characters
Codons
character
260
26
3 – 23 characters
Existing_variation
character
452
48
11 – 50 characters
DISTANCE
character
1
499
3 characters
TRANSCRIPT_STRAND
integer
2
0
-1 – 1mean 0.052
Min.
-1
1st Qu.
-1
Median
1
Mean
0.052
3rd Qu.
1
Max.
1
Std. dev
0.9996
Skewness
-0.1038
Kurtosis
-1.993
SYMBOL
character
467
0
2 – 11 characters
SYMBOL_SOURCE
character
2
0
4 – 24 characters
HGNC_ID
character
463
4
6 – 10 characters
BIOTYPE
character
8
0
5 – 20 characters
CANONICAL
character
1
127
3 characters
CCDS
character
426
48
8 – 11 characters
ENSP
character
460
7
15 characters
SWISSPROT
character
443
24
9 – 13 characters
TREMBL
character
92
406
9 – 13 characters
UNIPARC
character
460
7
13 characters
UNIPROT_ISOFORM
character
275
203
8 characters
RefSeq
character
430
42
11 – 251 characters
MANE
character
321
161
11 – 14 characters
APPRIS
character
6
33
2 characters
FLAGS
character
1
496
10 characters
SIFT
character
77
189
12 – 32 characters
PolyPhen
character
175
182
9 – 24 characters
EXON
character
254
19
3 – 7 characters
INTRON
character
18
482
3 – 6 characters
DOMAINS
character
453
40
13 – 4,362 characters
1000G_AF
character
2
496
5 characters
1000G_AFR_AF
character
2
496
1 – 6 characters
1000G_AMR_AF
character
1
496
1 characters
1000G_EAS_AF
character
1
496
1 characters
1000G_EUR_AF
character
2
496
1 – 5 characters
1000G_SAS_AF
character
2
496
1 – 5 characters
ESP_AA_AF
character
3
493
1 – 9 characters
ESP_EA_AF
character
5
493
1 – 9 characters
gnomAD_AF
character
53
427
1 – 9 characters
gnomAD_AFR_AF
character
11
427
1 – 9 characters
gnomAD_AMR_AF
character
14
427
1 – 9 characters
gnomAD_ASJ_AF
character
1
427
1 characters
gnomAD_EAS_AF
character
10
427
1 – 9 characters
gnomAD_FIN_AF
character
5
427
1 – 9 characters
gnomAD_NFE_AF
character
29
427
1 – 9 characters
gnomAD_OTH_AF
character
4
427
1 – 9 characters
gnomAD_SAS_AF
character
17
427
1 – 9 characters
MAX_AF
character
57
425
1 – 9 characters
MAX_AF_POPS
character
13
425
2 – 87 characters
gnomAD_non_cancer_AF
character
40
458
19 – 20 characters
gnomAD_non_cancer_AFR_AF
character
13
458
1 – 20 characters
gnomAD_non_cancer_AMI_AF
character
1
458
1 characters
gnomAD_non_cancer_AMR_AF
character
8
458
1 – 20 characters
gnomAD_non_cancer_ASJ_AF
character
1
458
1 characters
gnomAD_non_cancer_EAS_AF
character
5
458
1 – 19 characters
gnomAD_non_cancer_FIN_AF
character
4
458
1 – 20 characters
gnomAD_non_cancer_MID_AF
character
1
458
1 characters
gnomAD_non_cancer_NFE_AF
character
18
458
1 – 20 characters
gnomAD_non_cancer_OTH_AF
character
3
458
1 – 19 characters
gnomAD_non_cancer_SAS_AF
character
6
458
1 – 19 characters
gnomAD_non_cancer_MAX_AF_adj
character
12
487
18 – 20 characters
gnomAD_non_cancer_MAX_AF_POPS_adj
character
4
487
3 characters
CLIN_SIG
character
3
497
10 – 36 characters
SOMATIC
character
7
67
1 – 7 characters
PUBMED
character
2
498
8 characters
TRANSCRIPTION_FACTORS
character
0
500
–
MOTIF_NAME
character
0
500
–
MOTIF_POS
character
0
500
–
HIGH_INF_POS
character
0
500
–
MOTIF_SCORE_CHANGE
character
0
500
–
miRNA
character
1
499
10 characters
IMPACT
character
4
0
3 – 8 characters
PICK
integer
1
147
1
VARIANT_CLASS
character
4
0
3 – 9 characters
TSL
integer
5
62
1 – 5mean 1.694
Min.
1
1st Qu.
1
Median
1
Mean
1.6941
3rd Qu.
1
Max.
5
Std. dev
1.4486
Skewness
1.771
Kurtosis
1.269
Longest gap
3
HGVS_OFFSET
integer
5
494
1 – 6mean 3
Min.
1
1st Qu.
1.25
Median
2.5
Mean
3
3rd Qu.
4.5
Max.
6
Std. dev
2.0976
Skewness
0.325
Kurtosis
-1.881
Longest gap
123
Leading
103
Trailing
45
PHENO
character
6
66
1 – 7 characters
GENE_PHENO
character
1
314
1 characters
CONTEXT
character
499
0
11 – 31 characters
tumor_bam_uuid
character
274
0
36 characters
normal_bam_uuid
character
258
0
36 characters
case_id
character
258
0
36 characters
GDC_FILTER
character
1
492
9 characters
COSMIC
character
254
246
10 – 59 characters
hotspot
character
2
0
1 characters
RNA_Support
character
1
0
7 characters
RNA_depth
character
0
500
–
RNA_ref_count
character
0
500
–
RNA_alt_count
character
0
500
–
callers
character
6
0
12 – 25 characters
Version history
VersionReleasedSizeChangeStored asConfidence
3.232026-06-30500 × 141Unchangedrda · gzip
version 3 · 191 KB
exact
3.222025-12-09500 × 141Unchangedrda · gzip
version 3 · 191 KB
exact
3.212025-10-10500 × 141Unchangedrda · gzip
version 3 · 191 KB
exact
3.202024-10-29500 × 141Unchangedrda · gzip
version 3 · 191 KB
exact
3.192024-04-30500 × 141Unchangedrda · gzip
version 3 · 191 KB
exact
3.182023-10-24500 × 141–rda · gzip
version 3 · 191 KB
exact

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