Query

library(TCGAbiolinks)
query <- GDCquery(
    project = "TCGA-CHOL", 
    data.category = "Simple Nucleotide Variation", 
    access = "open", 
    legacy = FALSE, 
    data.type = "Masked Somatic Mutation", 
    workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)
query$results[[1]][,c("data_format","cases","sample_type","file_name")]
##    data_format                                                     cases
## 1          MAF TCGA-W5-AA2X-01A-11D-A417-09,TCGA-W5-AA2X-10A-01D-A41A-09
## 2          MAF TCGA-W5-AA33-01A-11D-A417-09,TCGA-W5-AA33-10A-01D-A41A-09
## 3          MAF TCGA-ZH-A8Y2-01A-11D-A417-09,TCGA-ZH-A8Y2-10A-01D-A41A-09
## 4          MAF TCGA-ZH-A8Y6-01A-11D-A417-09,TCGA-ZH-A8Y6-10A-01D-A41A-09
## 5          MAF TCGA-W5-AA2Z-01A-11D-A417-09,TCGA-W5-AA2Z-11A-11D-A41A-09
## 6          MAF TCGA-W7-A93N-01A-11D-A46P-09,TCGA-W7-A93N-11A-11D-A46P-09
## 7          MAF TCGA-W5-AA2Q-01A-11D-A417-09,TCGA-W5-AA2Q-10A-01D-A41A-09
## 8          MAF TCGA-4G-AAZT-01A-11D-A417-09,TCGA-4G-AAZT-10A-01D-A41A-09
## 9          MAF TCGA-W7-A93P-01A-12D-A46P-09,TCGA-W7-A93P-11A-11D-A46P-09
## 10         MAF TCGA-4G-AAZF-01A-12D-A46P-09,TCGA-4G-AAZF-11A-12D-A46P-09
## 11         MAF TCGA-W5-AA30-01A-31D-A417-09,TCGA-W5-AA30-10A-01D-A41A-09
## 12         MAF TCGA-W7-A93O-01A-31D-A46P-09,TCGA-W7-A93O-11A-11D-A46P-09
## 13         MAF TCGA-3X-AAV9-01A-72D-A417-09,TCGA-3X-AAV9-10A-01D-A41A-09
## 14         MAF TCGA-W6-AA0S-01A-11D-A417-09,TCGA-W6-AA0S-10A-01D-A41A-09
## 15         MAF TCGA-4G-AAZO-01A-12D-A417-09,TCGA-4G-AAZO-11A-11D-A41A-09
## 16         MAF TCGA-ZU-A8S4-01A-11D-A417-09,TCGA-ZU-A8S4-10A-01D-A41A-09
## 17         MAF TCGA-W5-AA39-01A-11D-A417-09,TCGA-W5-AA39-10A-01D-A41A-09
## 18         MAF TCGA-WD-A7RX-01A-12D-A417-09,TCGA-WD-A7RX-10A-01D-A41A-09
## 19         MAF TCGA-W5-AA2O-01A-11D-A417-09,TCGA-W5-AA2O-10A-01D-A41A-09
## 20         MAF TCGA-ZH-A8Y3-01A-11D-A46P-09,TCGA-ZH-A8Y3-10A-01D-A46P-09
## 21         MAF TCGA-W5-AA2W-01A-11D-A417-09,TCGA-W5-AA2W-10A-01D-A41A-09
## 22         MAF TCGA-W5-AA2R-01A-11D-A417-09,TCGA-W5-AA2R-10A-01D-A41A-09
## 23         MAF TCGA-W5-AA2G-01A-11D-A417-09,TCGA-W5-AA2G-10A-01D-A41A-09
## 24         MAF TCGA-W5-AA31-01A-11D-A417-09,TCGA-W5-AA31-10A-01D-A41A-09
## 25         MAF TCGA-ZH-A8Y7-01A-21D-A46P-09,TCGA-ZH-A8Y7-10A-01D-A46P-09
## 26         MAF TCGA-3X-AAVB-01A-31D-A417-09,TCGA-3X-AAVB-10A-01D-A41A-09
## 27         MAF TCGA-W5-AA2I-01A-32D-A417-09,TCGA-W5-AA2I-10A-01D-A41A-09
## 28         MAF TCGA-W5-AA2J-01A-31D-A46P-09,TCGA-W5-AA2J-10A-01D-A46P-09
## 29         MAF TCGA-W5-AA38-01A-11D-A417-09,TCGA-W5-AA38-10A-01D-A41A-09
## 30         MAF TCGA-4G-AAZR-01A-11D-A46P-09,TCGA-4G-AAZR-11A-11D-A46P-09
## 31         MAF TCGA-ZH-A8Y8-01A-51D-A417-09,TCGA-ZH-A8Y8-10A-01D-A41A-09
## 32         MAF TCGA-YR-A95A-01A-12D-A417-09,TCGA-YR-A95A-10A-01D-A41A-09
## 33         MAF TCGA-5A-A8ZF-01A-12D-A46P-09,TCGA-5A-A8ZF-10A-01D-A46P-09
## 34         MAF TCGA-W5-AA2K-01A-11D-A46P-09,TCGA-W5-AA2K-10A-01D-A46P-09
## 35         MAF TCGA-W5-AA2T-01A-12D-A417-09,TCGA-W5-AA2T-10A-01D-A41A-09
## 36         MAF TCGA-ZK-AAYZ-01A-12D-A46P-09,TCGA-ZK-AAYZ-10A-01D-A46P-09
## 37         MAF TCGA-ZH-A8Y4-01A-11D-A417-09,TCGA-ZH-A8Y4-10A-01D-A41A-09
## 38         MAF TCGA-ZH-A8Y5-01A-11D-A417-09,TCGA-ZH-A8Y5-10A-01D-A41A-09
## 39         MAF TCGA-W5-AA2U-01A-11D-A417-09,TCGA-W5-AA2U-10A-01D-A41A-09
## 40         MAF TCGA-W5-AA34-01A-11D-A417-09,TCGA-W5-AA34-10A-01D-A41A-09
## 41         MAF TCGA-ZH-A8Y1-01A-11D-A417-09,TCGA-ZH-A8Y1-10A-01D-A41A-09
## 42         MAF TCGA-W5-AA2H-01A-31D-A417-09,TCGA-W5-AA2H-10A-01D-A41A-09
## 43         MAF TCGA-5A-A8ZG-01A-11D-A46P-09,TCGA-5A-A8ZG-10A-01D-A46P-09
## 44         MAF TCGA-3X-AAVC-01A-21D-A417-09,TCGA-3X-AAVC-10A-01D-A41A-09
## 45         MAF TCGA-3X-AAVE-01A-11D-A417-09,TCGA-3X-AAVE-10A-01D-A41A-09
## 46         MAF TCGA-W5-AA36-01A-11D-A417-09,TCGA-W5-AA36-10A-01D-A41A-09
## 47         MAF TCGA-W5-AA2M-01A-11D-A46P-09,TCGA-W5-AA2M-10A-01D-A46P-09
## 48         MAF TCGA-3X-AAVA-01A-11D-A417-09,TCGA-3X-AAVA-10A-01D-A41A-09
## 49         MAF TCGA-4G-AAZG-01A-11D-A46P-09,TCGA-4G-AAZG-10A-01D-A46P-09
## 50         MAF TCGA-W6-AA0T-01A-31D-A46P-09,TCGA-W6-AA0T-10A-01D-A46P-09
## 51         MAF TCGA-ZD-A8I3-01A-11D-A417-09,TCGA-ZD-A8I3-10A-01D-A41A-09
##                           sample_type
## 1  Primary Tumor,Blood Derived Normal
## 2  Primary Tumor,Blood Derived Normal
## 3  Primary Tumor,Blood Derived Normal
## 4  Primary Tumor,Blood Derived Normal
## 5   Solid Tissue Normal,Primary Tumor
## 6   Solid Tissue Normal,Primary Tumor
## 7  Primary Tumor,Blood Derived Normal
## 8  Primary Tumor,Blood Derived Normal
## 9   Solid Tissue Normal,Primary Tumor
## 10  Solid Tissue Normal,Primary Tumor
## 11 Primary Tumor,Blood Derived Normal
## 12  Solid Tissue Normal,Primary Tumor
## 13 Primary Tumor,Blood Derived Normal
## 14 Primary Tumor,Blood Derived Normal
## 15  Solid Tissue Normal,Primary Tumor
## 16 Primary Tumor,Blood Derived Normal
## 17 Primary Tumor,Blood Derived Normal
## 18 Primary Tumor,Blood Derived Normal
## 19 Primary Tumor,Blood Derived Normal
## 20 Primary Tumor,Blood Derived Normal
## 21 Primary Tumor,Blood Derived Normal
## 22 Primary Tumor,Blood Derived Normal
## 23 Primary Tumor,Blood Derived Normal
## 24 Primary Tumor,Blood Derived Normal
## 25 Primary Tumor,Blood Derived Normal
## 26 Primary Tumor,Blood Derived Normal
## 27 Primary Tumor,Blood Derived Normal
## 28 Primary Tumor,Blood Derived Normal
## 29 Primary Tumor,Blood Derived Normal
## 30  Solid Tissue Normal,Primary Tumor
## 31 Primary Tumor,Blood Derived Normal
## 32 Primary Tumor,Blood Derived Normal
## 33 Primary Tumor,Blood Derived Normal
## 34 Primary Tumor,Blood Derived Normal
## 35 Primary Tumor,Blood Derived Normal
## 36 Primary Tumor,Blood Derived Normal
## 37 Primary Tumor,Blood Derived Normal
## 38 Primary Tumor,Blood Derived Normal
## 39 Primary Tumor,Blood Derived Normal
## 40 Primary Tumor,Blood Derived Normal
## 41 Primary Tumor,Blood Derived Normal
## 42 Primary Tumor,Blood Derived Normal
## 43 Primary Tumor,Blood Derived Normal
## 44 Primary Tumor,Blood Derived Normal
## 45 Primary Tumor,Blood Derived Normal
## 46 Primary Tumor,Blood Derived Normal
## 47 Primary Tumor,Blood Derived Normal
## 48 Primary Tumor,Blood Derived Normal
## 49 Primary Tumor,Blood Derived Normal
## 50 Primary Tumor,Blood Derived Normal
## 51 Primary Tumor,Blood Derived Normal
##                                                                  file_name
## 1  2ae3d770-d0ed-409a-a8ef-b7f63ce3299c.wxs.aliquot_ensemble_masked.maf.gz
## 2  8ec3ccfa-b0d2-4da6-bd40-cdf645681d09.wxs.aliquot_ensemble_masked.maf.gz
## 3  66144b4b-91cc-408a-843e-750cb9cfbf7c.wxs.aliquot_ensemble_masked.maf.gz
## 4  0e5eabd6-a5e7-44e4-bc81-198499c0615c.wxs.aliquot_ensemble_masked.maf.gz
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## 44 efb17d09-60f3-4be1-9511-b68e3de88379.wxs.aliquot_ensemble_masked.maf.gz
## 45 dc97b764-ef84-4294-9cc5-72bb7f1ed137.wxs.aliquot_ensemble_masked.maf.gz
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## 50 f746200d-8afd-4bb6-b6c1-395e977f8bbe.wxs.aliquot_ensemble_masked.maf.gz
## 51 829e8d08-feba-4f4b-bc45-77a9196280f2.wxs.aliquot_ensemble_masked.maf.gz

Download

GDCdownload(query)

Prepare

maf <- GDCprepare(query)

Data

dim(maf)
## [1] 3764  141
head(maf)
##   X1 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## 1  1       PLOD1           5351  WUGSC     GRCh38       chr1       11957858
## 2  1         IVL           3713  WUGSC     GRCh38       chr1      152910652
## 3  1       OBSCN          84033  WUGSC     GRCh38       chr1      228256740
## 4  1     MAP3K21          84451  WUGSC     GRCh38       chr1      233354868
## 5  1      LRRTM4          80059  WUGSC     GRCh38       chr2       77518314
## 6  1       MARCO           8685  WUGSC     GRCh38       chr2      118981468
##   End_Position Strand Variant_Classification Variant_Type Reference_Allele
## 1     11957858      +      Missense_Mutation          SNP                T
## 2    152910652      +      Nonsense_Mutation          SNP                C
## 3    228256740      +      Missense_Mutation          SNP                G
## 4    233354868      +      Missense_Mutation          SNP                T
## 5     77518314      +          Splice_Region          SNP                A
## 6    118981468      +      Missense_Mutation          SNP                C
##   Tumor_Seq_Allele1 Tumor_Seq_Allele2     dbSNP_RS dbSNP_Val_Status
## 1                 T                 C rs1286443479               NA
## 2                 C                 G         <NA>               NA
## 3                 G                 A         <NA>               NA
## 4                 T                 A        novel               NA
## 5                 A                 G        novel               NA
## 6                 C                 A        novel               NA
##           Tumor_Sample_Barcode  Matched_Norm_Sample_Barcode
## 1 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
## 2 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
## 3 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
## 4 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
## 5 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
## 6 TCGA-W5-AA2X-01A-11D-A417-09 TCGA-W5-AA2X-10A-01D-A41A-09
##   Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1
## 1                     NA                     NA                       NA
## 2                     NA                     NA                       NA
## 3                     NA                     NA                       NA
## 4                     NA                     NA                       NA
## 5                     NA                     NA                       NA
## 6                     NA                     NA                       NA
##   Tumor_Validation_Allele2 Match_Norm_Validation_Allele1
## 1                       NA                            NA
## 2                       NA                            NA
## 3                       NA                            NA
## 4                       NA                            NA
## 5                       NA                            NA
## 6                       NA                            NA
##   Match_Norm_Validation_Allele2 Verification_Status Validation_Status
## 1                            NA                  NA                NA
## 2                            NA                  NA                NA
## 3                            NA                  NA                NA
## 4                            NA                  NA                NA
## 5                            NA                  NA                NA
## 6                            NA                  NA                NA
##   Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score
## 1         Somatic               NA              NA                NA    NA
## 2         Somatic               NA              NA                NA    NA
## 3         Somatic               NA              NA                NA    NA
## 4         Somatic               NA              NA                NA    NA
## 5         Somatic               NA              NA                NA    NA
## 6         Somatic               NA              NA                NA    NA
##   BAM_File Sequencer                    Tumor_Sample_UUID
## 1       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
## 2       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
## 3       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
## 4       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
## 5       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
## 6       NA        NA afef815a-3e3b-497a-acf5-e9713ec6617f
##               Matched_Norm_Sample_UUID       HGVSc        HGVSp HGVSp_Short
## 1 ba2e4258-c494-4727-b7c4-7d24a61ce6ce    c.758T>C  p.Leu253Pro     p.L253P
## 2 ba2e4258-c494-4727-b7c4-7d24a61ce6ce    c.855C>G  p.Tyr285Ter     p.Y285*
## 3 ba2e4258-c494-4727-b7c4-7d24a61ce6ce   c.4399G>A p.Ala1467Thr    p.A1467T
## 4 ba2e4258-c494-4727-b7c4-7d24a61ce6ce   c.1168T>A  p.Ser390Thr     p.S390T
## 5 ba2e4258-c494-4727-b7c4-7d24a61ce6ce c.1551+4T>C         <NA>        <NA>
## 6 ba2e4258-c494-4727-b7c4-7d24a61ce6ce    c.826C>A  p.Gln276Lys     p.Q276K
##     Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth
## 1 ENST00000196061        8/19      46          31          15      44
## 2 ENST00000368764         2/2      63          44          19      57
## 3 ENST00000422127      15/105      40          36           4      36
## 4 ENST00000366624        4/10      58          21          37      48
## 5 ENST00000409093        <NA>      75          62          13      54
## 6 ENST00000327097        9/17      37          26          11      59
##   n_ref_count n_alt_count
## 1          NA          NA
## 2          NA          NA
## 3          NA          NA
## 4          NA          NA
## 5          NA          NA
## 6          NA          NA
##                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                all_effects
## 1                                                                                                                                                                                                                                                                                                PLOD1,missense_variant,p.L253P,ENST00000196061,NM_001316320.2&NM_000302.4,c.758T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.873),1;PLOD1,missense_variant,p.L255P,ENST00000429000,,c.764T>C,MODERATE,,deleterious(0),probably_damaging(0.986),1;PLOD1,non_coding_transcript_exon_variant,,ENST00000485046,,n.801T>C,MODIFIER,,,,1;PLOD1,downstream_gene_variant,,ENST00000358133,,,MODIFIER,,,,1;PLOD1,non_coding_transcript_exon_variant,,ENST00000465920,,n.708T>C,MODIFIER,,,,1
## 2                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                IVL,stop_gained,p.Y285*,ENST00000368764,NM_005547.3,c.855C>G,HIGH,YES,,,1
## 3 OBSCN,missense_variant,p.A1559T,ENST00000570156,NM_001271223.2,c.4675G>A,MODERATE,YES,tolerated(0.06),probably_damaging(0.998),1;OBSCN,missense_variant,p.A1467T,ENST00000662438,,c.4399G>A,MODERATE,,tolerated(0.06),possibly_damaging(0.885),1;OBSCN,missense_variant,p.A1467T,ENST00000422127,NM_001098623.2,c.4399G>A,MODERATE,,tolerated(0.28),probably_damaging(0.963),1;OBSCN,missense_variant,p.A1467T,ENST00000636476,,c.4399G>A,MODERATE,,,possibly_damaging(0.843),1;OBSCN,missense_variant,p.A1467T,ENST00000284548,NM_052843.4,c.4399G>A,MODERATE,,tolerated(0.44),probably_damaging(0.92),1;OBSCN,missense_variant,p.A1467T,ENST00000366704,,c.4399G>A,MODERATE,,deleterious(0),benign(0.018),1;AL353593.1,intron_variant,,ENST00000664490,,n.1659-16970C>T,MODIFIER,,,,-1
## 4                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                MAP3K21,missense_variant,p.S390T,ENST00000366624,NM_032435.3,c.1168T>A,MODERATE,YES,tolerated(0.13),benign(0.348),1;MAP3K21,missense_variant,p.S390T,ENST00000366623,,c.1168T>A,MODERATE,,tolerated(0.29),benign(0.061),1
## 5                                                                                                                                                                                                                                                                                          LRRTM4,stop_lost,p.*519Rext*21,ENST00000409088,NM_024993.6,c.1555T>C,HIGH,,,,-1;LRRTM4,stop_lost,p.*520Rext*21,ENST00000409282,NM_001282928.3,c.1558T>C,HIGH,,,,-1;LRRTM4,splice_region_variant,,ENST00000409093,NM_001282924.2,c.1551+4T>C,LOW,,,,-1;LRRTM4,splice_region_variant,,ENST00000409884,NM_001134745.2,c.1551+4T>C,LOW,,,,-1;LRRTM4,splice_region_variant,,ENST00000409911,NM_001330370.1,c.1554+4T>C,LOW,YES,,,-1;LRRTM4,downstream_gene_variant,,ENST00000456154,,,MODIFIER,,,,-1
## 6                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          MARCO,missense_variant,p.Q276K,ENST00000327097,NM_006770.3,c.826C>A,MODERATE,YES,tolerated(0.7),benign(0.096),1
##   Allele            Gene         Feature Feature_type       One_Consequence
## 1      C ENSG00000083444 ENST00000196061   Transcript      missense_variant
## 2      G ENSG00000163207 ENST00000368764   Transcript           stop_gained
## 3      A ENSG00000154358 ENST00000422127   Transcript      missense_variant
## 4      A ENSG00000143674 ENST00000366624   Transcript      missense_variant
## 5      G ENSG00000176204 ENST00000409093   Transcript splice_region_variant
## 6      A ENSG00000019169 ENST00000327097   Transcript      missense_variant
##                            Consequence cDNA_position CDS_position
## 1                     missense_variant      821/2976     758/2184
## 2                          stop_gained      918/2152     855/1758
## 3                     missense_variant    4473/24060   4399/23907
## 4                     missense_variant     1473/5853    1168/3111
## 5 splice_region_variant;intron_variant          <NA>         <NA>
## 6                     missense_variant      961/1838     826/1563
##   Protein_position Amino_acids  Codons Existing_variation DISTANCE
## 1          253/727         L/P cTg/cCg       rs1286443479       NA
## 2          285/585         Y/* taC/taG       COSV64216391       NA
## 3        1467/7968         A/T Gct/Act       COSV52808561       NA
## 4         390/1036         S/T Tcg/Acg               <NA>       NA
## 5             <NA>        <NA>    <NA>               <NA>       NA
## 6          276/520         Q/K Cag/Aag               <NA>       NA
##   TRANSCRIPT_STRAND  SYMBOL SYMBOL_SOURCE    HGNC_ID        BIOTYPE CANONICAL
## 1                 1   PLOD1          HGNC  HGNC:9081 protein_coding       YES
## 2                 1     IVL          HGNC  HGNC:6187 protein_coding       YES
## 3                 1   OBSCN          HGNC HGNC:15719 protein_coding      <NA>
## 4                 1 MAP3K21          HGNC HGNC:29798 protein_coding       YES
## 5                -1  LRRTM4          HGNC HGNC:19411 protein_coding      <NA>
## 6                 1   MARCO          HGNC  HGNC:6895 protein_coding       YES
##          CCDS            ENSP  SWISSPROT     TREMBL       UNIPARC
## 1   CCDS142.1 ENSP00000196061 Q02809.222       <NA> UPI000013C611
## 2  CCDS1030.1 ENSP00000357753 P07476.180       <NA> UPI000013E24A
## 3 CCDS58065.1 ENSP00000409493 Q5VST9.183       <NA> UPI0001838884
## 4  CCDS1598.1 ENSP00000355583 Q5TCX8.153       <NA> UPI000013D922
## 5 CCDS46346.1 ENSP00000386357 Q86VH4.133       <NA> UPI0000047808
## 6  CCDS2124.1 ENSP00000318916 Q9UEW3.172 Q4ZG40.128 UPI0000000DF8
##   UNIPROT_ISOFORM                     RefSeq        MANE APPRIS FLAGS
## 1        Q02809-1 NM_001316320.2;NM_000302.4 NM_000302.4     P1  <NA>
## 2            <NA>                NM_005547.3        <NA>     P1  <NA>
## 3        Q5VST9-1             NM_001098623.2        <NA>   <NA>  <NA>
## 4        Q5TCX8-1                NM_032435.3 NM_032435.3     P2  <NA>
## 5        Q86VH4-1             NM_001282924.2        <NA>     P4  <NA>
## 6        Q9UEW3-1                NM_006770.3        <NA>     P1  <NA>
##              SIFT                 PolyPhen   EXON INTRON
## 1  deleterious(0) possibly_damaging(0.873)   8/19   <NA>
## 2            <NA>                     <NA>    2/2   <NA>
## 3 tolerated(0.28) probably_damaging(0.963) 15/105   <NA>
## 4 tolerated(0.13)            benign(0.348)   4/10   <NA>
## 5            <NA>                     <NA>   <NA>    3/3
## 6  tolerated(0.7)            benign(0.096)   9/17   <NA>
##                                                                                                                                                                                           DOMAINS
## 1                                                                                                                                                         PANTHER:PTHR10730:SF5;PANTHER:PTHR10730
## 2                                                                                                                                                            Pfam:PF00904;MobiDB_lite:mobidb-lite
## 3                                    Gene3D:2.60.40.10;Pfam:PF07679;PROSITE_profiles:PS50835;PANTHER:PTHR44888;PANTHER:PTHR44888:SF2;SMART:SM00408;SMART:SM00409;Superfamily:SSF48726;CDD:cd00096
## 4 Gene3D:1.10.510.10;PDB-ENSP_mappings:4uya.A;Pfam:PF07714;PIRSF:PIRSF000556;Prints:PR00109;PROSITE_profiles:PS50011;PANTHER:PTHR23257;PANTHER:PTHR23257:SF750;SMART:SM00220;Superfamily:SSF56112
## 5                                                                                                                                                                                            <NA>
## 6                                                                                                                                                       PANTHER:PTHR24023:SF897;PANTHER:PTHR24023
##   1000G_AF 1000G_AFR_AF 1000G_AMR_AF 1000G_EAS_AF 1000G_EUR_AF 1000G_SAS_AF
## 1       NA           NA           NA           NA           NA           NA
## 2       NA           NA           NA           NA           NA           NA
## 3       NA           NA           NA           NA           NA           NA
## 4       NA           NA           NA           NA           NA           NA
## 5       NA           NA           NA           NA           NA           NA
## 6       NA           NA           NA           NA           NA           NA
##   ESP_AA_AF ESP_EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF
## 1        NA        NA 3.976e-06             0             0             0
## 2        NA        NA        NA            NA            NA            NA
## 3        NA        NA        NA            NA            NA            NA
## 4        NA        NA        NA            NA            NA            NA
## 5        NA        NA        NA            NA            NA            NA
## 6        NA        NA        NA            NA            NA            NA
##   gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF
## 1     5.437e-05             0             0             0             0
## 2            NA            NA            NA            NA            NA
## 3            NA            NA            NA            NA            NA
## 4            NA            NA            NA            NA            NA
## 5            NA            NA            NA            NA            NA
## 6            NA            NA            NA            NA            NA
##      MAX_AF MAX_AF_POPS gnomAD_non_cancer_AF gnomAD_non_cancer_AFR_AF
## 1 5.437e-05  gnomAD_EAS                   NA                       NA
## 2        NA        <NA>                   NA                       NA
## 3        NA        <NA>                   NA                       NA
## 4        NA        <NA>                   NA                       NA
## 5        NA        <NA>                   NA                       NA
## 6        NA        <NA>                   NA                       NA
##   gnomAD_non_cancer_AMI_AF gnomAD_non_cancer_AMR_AF gnomAD_non_cancer_ASJ_AF
## 1                       NA                       NA                       NA
## 2                       NA                       NA                       NA
## 3                       NA                       NA                       NA
## 4                       NA                       NA                       NA
## 5                       NA                       NA                       NA
## 6                       NA                       NA                       NA
##   gnomAD_non_cancer_EAS_AF gnomAD_non_cancer_FIN_AF gnomAD_non_cancer_MID_AF
## 1                       NA                       NA                       NA
## 2                       NA                       NA                       NA
## 3                       NA                       NA                       NA
## 4                       NA                       NA                       NA
## 5                       NA                       NA                       NA
## 6                       NA                       NA                       NA
##   gnomAD_non_cancer_NFE_AF gnomAD_non_cancer_OTH_AF gnomAD_non_cancer_SAS_AF
## 1                       NA                       NA                       NA
## 2                       NA                       NA                       NA
## 3                       NA                       NA                       NA
## 4                       NA                       NA                       NA
## 5                       NA                       NA                       NA
## 6                       NA                       NA                       NA
##   gnomAD_non_cancer_MAX_AF_adj gnomAD_non_cancer_MAX_AF_POPS_adj CLIN_SIG
## 1                           NA                              <NA>     <NA>
## 2                           NA                              <NA>     <NA>
## 3                           NA                              <NA>     <NA>
## 4                           NA                              <NA>     <NA>
## 5                           NA                              <NA>     <NA>
## 6                           NA                              <NA>     <NA>
##   SOMATIC PUBMED TRANSCRIPTION_FACTORS MOTIF_NAME MOTIF_POS HIGH_INF_POS
## 1    <NA>   <NA>                    NA         NA        NA           NA
## 2       1   <NA>                    NA         NA        NA           NA
## 3       1   <NA>                    NA         NA        NA           NA
## 4    <NA>   <NA>                    NA         NA        NA           NA
## 5    <NA>   <NA>                    NA         NA        NA           NA
## 6    <NA>   <NA>                    NA         NA        NA           NA
##   MOTIF_SCORE_CHANGE miRNA   IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO
## 1                 NA  <NA> MODERATE    1           SNV   1          NA  <NA>
## 2                 NA  <NA>     HIGH    1           SNV   2          NA     1
## 3                 NA  <NA> MODERATE   NA           SNV   5          NA     1
## 4                 NA  <NA> MODERATE    1           SNV   1          NA  <NA>
## 5                 NA  <NA>      LOW   NA           SNV   2          NA  <NA>
## 6                 NA  <NA> MODERATE    1           SNV   1          NA  <NA>
##   GENE_PHENO     CONTEXT                       tumor_bam_uuid
## 1          1 CTACCTGGGCA 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
## 2         NA AAGTACCTGGA 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
## 3         NA AGGTGGCTCAG 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
## 4         NA GTCCATCGTTT 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
## 5         NA GGTTCATACCT 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
## 6         NA GAGCCCAGGGG 341bc32a-c6c0-4b06-944a-36ed9d7f68c1
##                        normal_bam_uuid                              case_id
## 1 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
## 2 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
## 3 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
## 4 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
## 5 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
## 6 0e0df451-450d-4698-bc16-c36e5bfb0681 6e534dd3-81ac-4575-ab1e-02c21e10916d
##   GDC_FILTER COSMIC hotspot RNA_Support RNA_depth RNA_ref_count RNA_alt_count
## 1       <NA>   <NA>       N     Unknown        NA            NA            NA
## 2       <NA>   <NA>       N     Unknown        NA            NA            NA
## 3       <NA>   <NA>       N     Unknown        NA            NA            NA
## 4       <NA>   <NA>       N     Unknown        NA            NA            NA
## 5       <NA>   <NA>       N     Unknown        NA            NA            NA
## 6       <NA>   <NA>       N     Unknown        NA            NA            NA
##                 callers
## 1 muse;mutect2;varscan2
## 2 muse;mutect2;varscan2
## 3          muse;mutect2
## 4 muse;mutect2;varscan2
## 5 muse;mutect2;varscan2
## 6 muse;mutect2;varscan2

sessionInfo

sessionInfo()
## R version 4.2.0 (2022-04-22)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Big Sur/Monterey 10.16
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] TCGAbiolinks_2.25.0
## 
## loaded via a namespace (and not attached):
##  [1] bitops_1.0-7                matrixStats_0.62.0         
##  [3] bit64_4.0.5                 filelock_1.0.2             
##  [5] progress_1.2.2              httr_1.4.3                 
##  [7] GenomeInfoDb_1.32.2         tools_4.2.0                
##  [9] bslib_0.3.1                 utf8_1.2.2                 
## [11] R6_2.5.1                    DBI_1.1.2                  
## [13] BiocGenerics_0.42.0         colorspace_2.0-3           
## [15] withr_2.5.0                 tidyselect_1.1.2           
## [17] prettyunits_1.1.1           bit_4.0.4                  
## [19] curl_4.3.2                  compiler_4.2.0             
## [21] cli_3.3.0                   rvest_1.0.2                
## [23] Biobase_2.56.0              xml2_1.3.3                 
## [25] DelayedArray_0.22.0         sass_0.4.1                 
## [27] scales_1.2.0                readr_2.1.2                
## [29] rappdirs_0.3.3              stringr_1.4.0              
## [31] digest_0.6.29               rmarkdown_2.14             
## [33] XVector_0.36.0              pkgconfig_2.0.3            
## [35] htmltools_0.5.2             MatrixGenerics_1.8.0       
## [37] dbplyr_2.2.0                fastmap_1.1.0              
## [39] rlang_1.0.2                 rstudioapi_0.13            
## [41] RSQLite_2.2.14              prettydoc_0.4.1            
## [43] jquerylib_0.1.4             generics_0.1.2             
## [45] jsonlite_1.8.0              vroom_1.5.7                
## [47] dplyr_1.0.9                 RCurl_1.98-1.7             
## [49] magrittr_2.0.3              GenomeInfoDbData_1.2.8     
## [51] Matrix_1.4-1                Rcpp_1.0.8.3               
## [53] munsell_0.5.0               S4Vectors_0.34.0           
## [55] fansi_1.0.3                 lifecycle_1.0.1            
## [57] stringi_1.7.6               yaml_2.3.5                 
## [59] SummarizedExperiment_1.26.1 zlibbioc_1.42.0            
## [61] plyr_1.8.7                  BiocFileCache_2.4.0        
## [63] grid_4.2.0                  blob_1.2.3                 
## [65] parallel_4.2.0              crayon_1.5.1               
## [67] lattice_0.20-45             Biostrings_2.64.0          
## [69] hms_1.1.1                   KEGGREST_1.36.2            
## [71] knitr_1.39                  pillar_1.7.0               
## [73] GenomicRanges_1.48.0        TCGAbiolinksGUI.data_1.16.0
## [75] biomaRt_2.52.0              stats4_4.2.0               
## [77] XML_3.99-0.10               glue_1.6.2                 
## [79] evaluate_0.15               downloader_0.4             
## [81] data.table_1.14.2           png_0.1-7                  
## [83] vctrs_0.4.1                 tzdb_0.3.0                 
## [85] gtable_0.3.0                purrr_0.3.4                
## [87] tidyr_1.2.0                 assertthat_0.2.1           
## [89] cachem_1.0.6                ggplot2_3.3.6              
## [91] xfun_0.31                   tibble_3.1.7               
## [93] AnnotationDbi_1.58.0        memoise_2.0.1              
## [95] IRanges_2.30.0              ellipsis_0.3.2