TCGA-STAD
query <- GDCquery(
project = "TCGA-STAD",
data.category = "Simple Nucleotide Variation",
access = "open",
legacy = FALSE,
data.type = "Masked Somatic Mutation",
workflow.type = "Aliquot Ensemble Somatic Variant Merging and Masking"
)GDCdownload(query)
maf <- GDCprepare(query)problems()
dim(maf)## [1] 183107 141head(maf)## X1 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## 1 1 C1orf174 339448 BI GRCh38 chr1 3890597
## 2 1 PRAMEF15 653619 BI GRCh38 chr1 13319520
## 3 1 CASP9 842 BI GRCh38 chr1 15504725
## 4 1 ERI3 79033 BI GRCh38 chr1 44221639
## 5 1 ELAVL4 1996 BI GRCh38 chr1 50193874
## 6 1 ADGRL2 23266 BI GRCh38 chr1 81990792
## End_Position Strand Variant_Classification Variant_Type Reference_Allele
## 1 3890597 + Missense_Mutation SNP C
## 2 13319520 + Frame_Shift_Del DEL C
## 3 15504725 + Missense_Mutation SNP C
## 4 44221639 + Splice_Region SNP G
## 5 50193874 + Missense_Mutation SNP A
## 6 81990792 + Missense_Mutation SNP G
## Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status
## 1 C T rs776552583 <NA>
## 2 C - novel <NA>
## 3 C T rs754180617 <NA>
## 4 G A rs773605425 <NA>
## 5 A G <NA> <NA>
## 6 G C <NA> <NA>
## Tumor_Sample_Barcode Matched_Norm_Sample_Barcode
## 1 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 2 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 3 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 4 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 5 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 6 TCGA-BR-8484-01A-11D-2394-08 TCGA-BR-8484-10A-01D-2394-08
## 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> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## 2 <NA> <NA> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## 3 <NA> <NA> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## 4 <NA> <NA> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## 5 <NA> <NA> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## 6 <NA> <NA> 6f00fcf3-f10e-4c22-b4ea-d9cc765d2647
## Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short
## 1 fb53f86c-6077-4496-a222-35622ccdedf8 c.590G>A p.Arg197Gln p.R197Q
## 2 fb53f86c-6077-4496-a222-35622ccdedf8 c.444del p.Leu149Ter p.L149*
## 3 fb53f86c-6077-4496-a222-35622ccdedf8 c.754G>A p.Gly252Ser p.G252S
## 4 fb53f86c-6077-4496-a222-35622ccdedf8 c.933C>T p.Asp311= p.D311=
## 5 fb53f86c-6077-4496-a222-35622ccdedf8 c.464A>G p.Tyr155Cys p.Y155C
## 6 fb53f86c-6077-4496-a222-35622ccdedf8 c.4027G>C p.Val1343Leu p.V1343L
## Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth
## 1 ENST00000361605 3/4 117 57 60 113
## 2 ENST00000376152 3/4 917 827 89 604
## 3 ENST00000333868 6/9 111 100 11 100
## 4 ENST00000372257 9/9 44 38 6 70
## 5 ENST00000371823 4/7 181 172 8 178
## 6 ENST00000370717 22/22 118 106 12 124
## 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 C1orf174,missense_variant,p.R197Q,ENST00000361605,NM_207356.3,c.590G>A,MODERATE,YES,deleterious(0.04),possibly_damaging(0.536),-1;C1orf174,non_coding_transcript_exon_variant,,ENST00000486765,,n.1540G>A,MODIFIER,,,,-1;C1orf174,non_coding_transcript_exon_variant,,ENST00000474140,,n.2522G>A,MODIFIER,,,,-1
## 2 PRAMEF15,frameshift_variant,p.L149*,ENST00000376152,NM_001098376.3,c.444del,HIGH,YES,,,1;AC243961.1,upstream_gene_variant,,ENST00000432559,,,MODIFIER,YES,,,1
## 3 CASP9,missense_variant,p.G252S,ENST00000546424,,c.754G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.995),-1;CASP9,missense_variant,p.G252S,ENST00000333868,NM_001229.5,c.754G>A,MODERATE,,deleterious(0.04),probably_damaging(0.996),-1;CASP9,missense_variant,p.G169S,ENST00000375890,NM_032996.3,c.505G>A,MODERATE,,deleterious(0.02),probably_damaging(0.996),-1;CASP9,missense_variant,p.G169S,ENST00000447522,,c.505G>A,MODERATE,,deleterious(0.04),probably_damaging(0.996),-1;CASP9,missense_variant,p.G222S,ENST00000440484,,c.664G>A,MODERATE,,deleterious(0),possibly_damaging(0.899),-1;CASP9,missense_variant,p.G94S,ENST00000424908,,c.280G>A,MODERATE,,deleterious(0),possibly_damaging(0.862),-1;CASP9,intron_variant,,ENST00000348549,NM_001278054.1,c.419-9273G>A,MODIFIER,,,,-1;CASP9,3_prime_UTR_variant,,ENST00000400777,,c.*347G>A,MODIFIER,,,,-1;CASP9,3_prime_UTR_variant,,ENST00000474305,,c.*326G>A,MODIFIER,,,,-1;CASP9,downstream_gene_variant,,ENST00000546969,,,MODIFIER,,,,-1
## 4 ERI3,splice_region_variant,p.D311=,ENST00000372257,NM_001301699.1&NM_001301700.1&NM_001301698.2&NM_024066.3,c.933C>T,LOW,YES,,,-1;ERI3,splice_region_variant,,ENST00000649995,,c.*134C>T,LOW,,,,-1;ERI3,splice_region_variant,p.D196=,ENST00000372259,,c.588C>T,LOW,,,,-1;ERI3,splice_region_variant,p.D176=,ENST00000456170,NM_001301701.1,c.528C>T,LOW,,,,-1;ERI3,splice_region_variant,,ENST00000479101,,c.*10C>T,LOW,,,,-1;DMAP1,downstream_gene_variant,,ENST00000315913,NM_001034023.2,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000361745,NM_001034024.2,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000372289,NM_019100.5,,MODIFIER,YES,,,1;DMAP1,downstream_gene_variant,,ENST00000372290,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000437511,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000440641,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000446292,,,MODIFIER,,,,1;ERI3,splice_region_variant,,ENST00000462341,,n.274C>T,LOW,,,,-1;DMAP1,downstream_gene_variant,,ENST00000471829,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000483741,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000487922,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000488433,,,MODIFIER,,,,1;DMAP1,downstream_gene_variant,,ENST00000494092,,,MODIFIER,,,,1;ERI3,splice_region_variant,,ENST00000489710,,c.*97C>T,LOW,,,,-1
## 5 ELAVL4,missense_variant,p.Y148C,ENST00000652274,,c.443A>G,MODERATE,,tolerated(0.23),benign(0.066),1;ELAVL4,missense_variant,p.Y155C,ENST00000371824,NM_001144774.3,c.464A>G,MODERATE,,tolerated(0.23),benign(0.102),1;ELAVL4,missense_variant,p.Y160C,ENST00000371821,NM_001324213.2,c.479A>G,MODERATE,,tolerated(0.21),benign(0.242),1;ELAVL4,missense_variant,p.Y155C,ENST00000371827,NM_001144776.3,c.464A>G,MODERATE,,tolerated(0.23),benign(0.024),1;ELAVL4,missense_variant,p.Y160C,ENST00000371819,NM_001294348.2&NM_001324215.2,c.479A>G,MODERATE,,tolerated(0.24),benign(0.066),1;ELAVL4,missense_variant,p.Y155C,ENST00000650764,,c.464A>G,MODERATE,,tolerated(0.23),probably_damaging(0.987),1;ELAVL4,missense_variant,p.Y168C,ENST00000651347,,c.503A>G,MODERATE,,tolerated(0.23),probably_damaging(0.93),1;ELAVL4,missense_variant,p.Y158C,ENST00000448907,NM_001324208.2&NM_001144777.3,c.473A>G,MODERATE,,tolerated(0.24),benign(0.03),1;ELAVL4,missense_variant,p.Y155C,ENST00000371823,NM_021952.5,c.464A>G,MODERATE,,tolerated(0.21),benign(0.066),1;ELAVL4,missense_variant,p.Y191C,ENST00000357083,NM_001144775.3,c.572A>G,MODERATE,YES,tolerated(0.22),probably_damaging(0.998),1;ELAVL4,missense_variant,p.Y154C,ENST00000651258,NM_001324212.2&NM_001324209.2&NM_001324214.2,c.461A>G,MODERATE,,tolerated(0.23),probably_damaging(0.93),1;ELAVL4,missense_variant,p.Y99C,ENST00000652353,,c.296A>G,MODERATE,,tolerated(0.21),benign(0.066),1;ELAVL4,non_coding_transcript_exon_variant,,ENST00000474675,,n.173A>G,MODIFIER,,,,1
## 6 ADGRL2,missense_variant,p.V1343L,ENST00000370728,NM_001366003.1&NM_001366004.1,c.4027G>C,MODERATE,,tolerated(0.64),benign(0.145),1;ADGRL2,missense_variant,p.V1300L,ENST00000370730,,c.3898G>C,MODERATE,,tolerated_low_confidence(0.61),probably_damaging(0.981),1;ADGRL2,missense_variant,p.V1354L,ENST00000674307,,c.4060G>C,MODERATE,,tolerated(0.62),benign(0.046),1;ADGRL2,missense_variant,p.V1343L,ENST00000370717,NM_001366005.1&NM_001366006.1&NM_001350698.2,c.4027G>C,MODERATE,,tolerated(0.64),benign(0.145),1;ADGRL2,missense_variant,p.V1330L,ENST00000674209,,c.3988G>C,MODERATE,,tolerated(0.64),benign(0.168),1;ADGRL2,missense_variant,p.V1315L,ENST00000627151,,c.3943G>C,MODERATE,,tolerated_low_confidence(0.64),benign(0.007),1;ADGRL2,missense_variant,p.V1302L,ENST00000674168,,c.3904G>C,MODERATE,,tolerated_low_confidence(0.6),benign(0.069),1;ADGRL2,missense_variant,p.V1300L,ENST00000674419,NM_001330645.2,c.3898G>C,MODERATE,,tolerated_low_confidence(0.61),probably_damaging(0.981),1;ADGRL2,missense_variant,p.V1287L,ENST00000674393,NM_001366002.1,c.3859G>C,MODERATE,,tolerated_low_confidence(0.61),benign(0.089),1;ADGRL2,missense_variant,p.V1287L,ENST00000319517,NM_012302.4,c.3859G>C,MODERATE,,tolerated_low_confidence(0.61),benign(0.089),1;ADGRL2,missense_variant,p.V1358L,ENST00000370725,NM_001366007.1,c.4072G>C,MODERATE,YES,tolerated(0.63),benign(0.018),1;ADGRL2,missense_variant,p.V1345L,ENST00000370723,,c.4033G>C,MODERATE,,tolerated(0.66),benign(0.01),1;ADGRL2,missense_variant,p.V1315L,ENST00000370727,,c.3943G>C,MODERATE,,tolerated_low_confidence(0.64),benign(0.007),1;ADGRL2,missense_variant,p.V1268L,ENST00000370721,,c.3802G>C,MODERATE,,tolerated_low_confidence(0.55),benign(0.01),1;ADGRL2,missense_variant,p.V1287L,ENST00000359929,NM_001297704.2,c.3859G>C,MODERATE,,tolerated_low_confidence(0.61),benign(0.089),1;ADGRL2,missense_variant,p.V1235L,ENST00000449420,,c.3703G>C,MODERATE,,tolerated(0.62),benign(0.018),1;ADGRL2,missense_variant,p.V355L,ENST00000402328,,c.1063G>C,MODERATE,,tolerated(0.67),benign(0.003),1;ADGRL2,3_prime_UTR_variant,,ENST00000370715,NM_001297705.2,c.*431G>C,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000674442,NM_001350699.2,c.*449G>C,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000370713,NM_001297706.2,c.*390G>C,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000674407,NM_001366008.1,c.*403G>C,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000674208,NM_001366009.1,c.*390G>C,MODIFIER,,,,1;ADGRL2,downstream_gene_variant,,ENST00000674489,,,MODIFIER,,,,1;ADGRL2,non_coding_transcript_exon_variant,,ENST00000469377,,n.1507G>C,MODIFIER,,,,1;ADGRL2,downstream_gene_variant,,ENST00000464551,,,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000674492,,c.*4516G>C,MODIFIER,,,,1;ADGRL2,3_prime_UTR_variant,,ENST00000674373,,c.*4463G>C,MODIFIER,,,,1;ADGRL2,non_coding_transcript_exon_variant,,ENST00000472424,,n.7169G>C,MODIFIER,,,,1;ADGRL2,non_coding_transcript_exon_variant,,ENST00000674198,,n.5349G>C,MODIFIER,,,,1;ADGRL2,non_coding_transcript_exon_variant,,ENST00000464775,,n.2317G>C,MODIFIER,,,,1;ADGRL2,downstream_gene_variant,,ENST00000674464,,,MODIFIER,,,,1
## Allele Gene Feature Feature_type One_Consequence
## 1 T ENSG00000198912 ENST00000361605 Transcript missense_variant
## 2 - ENSG00000204501 ENST00000376152 Transcript frameshift_variant
## 3 T ENSG00000132906 ENST00000333868 Transcript missense_variant
## 4 A ENSG00000117419 ENST00000372257 Transcript splice_region_variant
## 5 G ENSG00000162374 ENST00000371823 Transcript missense_variant
## 6 C ENSG00000117114 ENST00000370717 Transcript missense_variant
## Consequence cDNA_position CDS_position
## 1 missense_variant 676/1645 590/732
## 2 frameshift_variant 536/1865 442/1437
## 3 missense_variant 769/2808 754/1251
## 4 splice_region_variant;synonymous_variant 1164/1733 933/1014
## 5 missense_variant 688/1591 464/1143
## 6 missense_variant 4243/5873 4027/4380
## Protein_position Amino_acids Codons Existing_variation DISTANCE
## 1 197/243 R/Q cGg/cAg rs776552583;COSV64365894 <NA>
## 2 148/478 P/X Ccc/cc <NA> <NA>
## 3 252/416 G/S Ggc/Agc rs754180617;COSV61601602 <NA>
## 4 311/337 D gaC/gaT rs773605425;COSV59999922 <NA>
## 5 155/380 Y/C tAc/tGc COSV63916278 <NA>
## 6 1343/1459 V/L Gtg/Ctg COSV54670735 <NA>
## TRANSCRIPT_STRAND SYMBOL SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL
## 1 -1 C1orf174 HGNC HGNC:27915 protein_coding YES
## 2 1 PRAMEF15 HGNC HGNC:26764 protein_coding YES
## 3 -1 CASP9 HGNC HGNC:1511 protein_coding <NA>
## 4 -1 ERI3 HGNC HGNC:17276 protein_coding YES
## 5 1 ELAVL4 HGNC HGNC:3315 protein_coding <NA>
## 6 1 ADGRL2 HGNC HGNC:18582 protein_coding <NA>
## CCDS ENSP SWISSPROT TREMBL UNIPARC UNIPROT_ISOFORM
## 1 CCDS53.1 ENSP00000355306 Q8IYL3.122 <NA> UPI00001C1D98 <NA>
## 2 CCDS44059.1 ENSP00000365322 Q5VWM5.129 <NA> UPI0000199BA7 <NA>
## 3 CCDS158.1 ENSP00000330237 P55211.221 <NA> UPI000012D14F P55211-1
## 4 CCDS30696.1 ENSP00000361331 O43414.140 <NA> UPI00001C1D9B O43414-1
## 5 CCDS553.1 ENSP00000360888 P26378.182 <NA> UPI000047014C P26378-1
## 6 <NA> ENSP00000359752 O95490.170 <NA> UPI00003588C3 O95490-1
## RefSeq MANE
## 1 NM_207356.3 NM_207356.3
## 2 NM_001098376.3 NM_001098376.3
## 3 NM_001229.5 NM_001229.5
## 4 NM_001301699.1;NM_001301700.1;NM_001301698.2;NM_024066.3 NM_024066.3
## 5 NM_021952.5 <NA>
## 6 NM_001366005.1;NM_001366006.1;NM_001350698.2 <NA>
## APPRIS FLAGS SIFT PolyPhen EXON INTRON
## 1 P1 <NA> deleterious(0.04) possibly_damaging(0.536) 3/4 <NA>
## 2 P1 <NA> <NA> <NA> 3/4 <NA>
## 3 P1 <NA> deleterious(0.04) probably_damaging(0.996) 6/9 <NA>
## 4 P1 <NA> <NA> <NA> 9/9 <NA>
## 5 P4 <NA> tolerated(0.21) benign(0.066) 4/7 <NA>
## 6 P3 <NA> tolerated(0.64) benign(0.145) 22/22 <NA>
## DOMAINS
## 1 Pfam:PF15772;PANTHER:PTHR28491
## 2 PIRSF:PIRSF038286;PANTHER:PTHR14224;PANTHER:PTHR14224:SF19
## 3 PDB-ENSP_mappings:1jxq.A;PDB-ENSP_mappings:1jxq.B;PDB-ENSP_mappings:1jxq.C;PDB-ENSP_mappings:1jxq.D;PDB-ENSP_mappings:1nw9.B;PDB-ENSP_mappings:2ar9.A;PDB-ENSP_mappings:2ar9.B;PDB-ENSP_mappings:2ar9.C;PDB-ENSP_mappings:2ar9.D;PDB-ENSP_mappings:3v3k.A;PDB-ENSP_mappings:3v3k.C;PDB-ENSP_mappings:3v3k.E;PDB-ENSP_mappings:3v3k.G;PDB-ENSP_mappings:3v3k.I;PDB-ENSP_mappings:3v3k.K;PDB-ENSP_mappings:3v3k.M;PDB-ENSP_mappings:3v3k.O;CDD:cd00032;PIRSF:PIRSF038001;Pfam:PF00656;Gene3D:3.40.50.1460;SMART:SM00115;Superfamily:SSF52129;PROSITE_profiles:PS50208;PANTHER:PTHR10454;PANTHER:PTHR10454:SF157
## 4 PDB-ENSP_mappings:2xri.A;CDD:cd06133;PANTHER:PTHR23044;PANTHER:PTHR23044:SF61;Gene3D:3.30.420.10;Pfam:PF00929;SMART:SM00479;Superfamily:SSF53098
## 5 PDB-ENSP_mappings:1fxl.A;PDB-ENSP_mappings:1g2e.A;PROSITE_profiles:PS50102;PANTHER:PTHR10352;PANTHER:PTHR10352:SF9;Pfam:PF00076;Gene3D:3.30.70.330;TIGRFAM:TIGR01661;SMART:SM00360;Superfamily:SSF54928;Prints:PR00961
## 6 Pfam:PF02354
## 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> 1.194e-05 0 0 9.929e-05
## 2 <NA> <NA> <NA> <NA> <NA> <NA>
## 3 <NA> <NA> 1.991e-05 0 0 0
## 4 <NA> <NA> 8.022e-06 0 0 0
## 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 0 0 8.802e-06 0 3.266e-05
## 2 <NA> <NA> <NA> <NA> <NA>
## 3 5.439e-05 0 3.523e-05 0 0
## 4 0 0 1.791e-05 0 0
## 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 9.929e-05 gnomAD_ASJ 6.76370018481975e-06 0
## 2 <NA> <NA> <NA> <NA>
## 3 5.439e-05 gnomAD_EAS 6.75941009831149e-06 0
## 4 1.791e-05 gnomAD_NFE <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 0 0 0
## 2 <NA> <NA> <NA>
## 3 0 0 0
## 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 0.00020169399795122 0 0
## 2 <NA> <NA> <NA>
## 3 0 0 0
## 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 0 0 0
## 2 <NA> <NA> <NA>
## 3 1.54306999320397e-05 0 0
## 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 0;1 <NA> <NA> <NA> <NA> <NA>
## 2 <NA> <NA> <NA> <NA> <NA> <NA>
## 3 0;1 <NA> <NA> <NA> <NA> <NA>
## 4 0;1 <NA> <NA> <NA> <NA> <NA>
## 5 1 <NA> <NA> <NA> <NA> <NA>
## 6 1 <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 0;1
## 2 <NA> <NA> HIGH 1 deletion 1 2 <NA>
## 3 <NA> <NA> MODERATE NA SNV 1 NA 0;1
## 4 <NA> <NA> LOW 1 SNV 1 NA 0;1
## 5 <NA> <NA> MODERATE NA SNV 1 NA 1
## 6 <NA> <NA> MODERATE NA SNV 5 NA 1
## GENE_PHENO CONTEXT tumor_bam_uuid
## 1 <NA> AGAACCGGCTC 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## 2 <NA> CGGCAGCCCTTG 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## 3 1 TGTGCCGTAGA 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## 4 <NA> CAGTCGTCTAA 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## 5 <NA> GCAATACGGCC 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## 6 <NA> AGAAAGTGAAG 50ff1dfa-e62a-4e4e-bf47-483b4119000b
## normal_bam_uuid case_id
## 1 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## 2 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## 3 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## 4 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## 5 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## 6 0cbefe56-f26b-4aa4-9b2e-85fb5ae347db fa00a6a7-d5b0-40b9-8360-d56f7db64d34
## GDC_FILTER COSMIC hotspot RNA_Support RNA_depth
## 1 <NA> COSM4007588 N Unknown <NA>
## 2 <NA> <NA> N Unknown <NA>
## 3 <NA> COSM4023672 N Unknown <NA>
## 4 <NA> COSM4008370;COSM4008371;COSM681230 N Unknown <NA>
## 5 <NA> COSM4008689;COSM4008690 N Unknown <NA>
## 6 <NA> COSM4010152;COSM4010153;COSM4010154 N Unknown <NA>
## RNA_ref_count RNA_alt_count callers
## 1 <NA> <NA> muse;mutect2;varscan2
## 2 <NA> <NA> mutect2;pindel;varscan2
## 3 <NA> <NA> muse;mutect2;varscan2
## 4 <NA> <NA> muse;varscan2
## 5 <NA> <NA> muse;mutect2
## 6 <NA> <NA> muse;mutect2Session information
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.0 (2022-04-22)
## os macOS Big Sur/Monterey 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/Sao_Paulo
## date 2022-07-06
## pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date (UTC) lib source
## AnnotationDbi 1.58.0 2022-04-26 [1] Bioconductor
## assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.2.0)
## Biobase 2.56.0 2022-04-26 [1] Bioconductor
## BiocFileCache 2.4.0 2022-04-26 [1] Bioconductor
## BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
## biomaRt 2.52.0 2022-04-26 [1] Bioconductor
## Biostrings 2.64.0 2022-04-26 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.0)
## bit64 4.0.5 2020-08-30 [1] CRAN (R 4.2.0)
## bitops 1.0-7 2021-04-24 [1] CRAN (R 4.2.0)
## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.2.0)
## cachem 1.0.6 2021-08-19 [1] CRAN (R 4.2.0)
## callr 3.7.0 2021-04-20 [1] CRAN (R 4.2.0)
## cli 3.3.0 2022-04-25 [1] CRAN (R 4.2.0)
## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
## crayon 1.5.1 2022-03-26 [1] CRAN (R 4.2.0)
## curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0)
## data.table 1.14.2 2021-09-27 [1] CRAN (R 4.2.0)
## DBI 1.1.3 2022-06-18 [1] CRAN (R 4.2.0)
## dbplyr 2.2.1 2022-06-27 [1] CRAN (R 4.2.0)
## DelayedArray 0.22.0 2022-04-26 [1] Bioconductor
## desc 1.4.1 2022-03-06 [1] CRAN (R 4.2.0)
## devtools 2.4.3 2021-11-30 [1] CRAN (R 4.2.0)
## digest 0.6.29 2021-12-01 [1] CRAN (R 4.2.0)
## downloader 0.4 2015-07-09 [1] CRAN (R 4.2.0)
## dplyr 1.0.9 2022-04-28 [1] CRAN (R 4.2.0)
## ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.2.0)
## evaluate 0.15 2022-02-18 [1] CRAN (R 4.2.0)
## fansi 1.0.3 2022-03-24 [1] CRAN (R 4.2.0)
## fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.0)
## filelock 1.0.2 2018-10-05 [1] CRAN (R 4.2.0)
## fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.0)
## generics 0.1.3 2022-07-05 [1] CRAN (R 4.2.0)
## GenomeInfoDb 1.32.2 2022-05-15 [1] Bioconductor
## GenomeInfoDbData 1.2.8 2022-06-17 [1] Bioconductor
## GenomicRanges 1.48.0 2022-04-26 [1] Bioconductor
## ggplot2 3.3.6 2022-05-03 [1] CRAN (R 4.2.0)
## glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.0)
## gtable 0.3.0 2019-03-25 [1] CRAN (R 4.2.0)
## hms 1.1.1 2021-09-26 [1] CRAN (R 4.2.0)
## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0)
## httr 1.4.3 2022-05-04 [1] CRAN (R 4.2.0)
## IRanges 2.30.0 2022-04-26 [1] Bioconductor
## jquerylib 0.1.4 2021-04-26 [1] CRAN (R 4.2.0)
## jsonlite 1.8.0 2022-02-22 [1] CRAN (R 4.2.0)
## KEGGREST 1.36.2 2022-06-09 [1] Bioconductor
## knitr 1.39 2022-04-26 [1] CRAN (R 4.2.0)
## lattice 0.20-45 2021-09-22 [1] CRAN (R 4.2.0)
## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
## MatrixGenerics 1.8.1 2022-06-26 [1] Bioconductor
## matrixStats 0.62.0 2022-04-19 [1] CRAN (R 4.2.0)
## memoise 2.0.1 2021-11-26 [1] CRAN (R 4.2.0)
## munsell 0.5.0 2018-06-12 [1] CRAN (R 4.2.0)
## pillar 1.7.0 2022-02-01 [1] CRAN (R 4.2.0)
## pkgbuild 1.3.1 2021-12-20 [1] CRAN (R 4.2.0)
## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
## pkgload 1.3.0 2022-06-27 [1] CRAN (R 4.2.0)
## plyr 1.8.7 2022-03-24 [1] CRAN (R 4.2.0)
## png 0.1-7 2013-12-03 [1] CRAN (R 4.2.0)
## prettydoc 0.4.1 2021-01-10 [1] CRAN (R 4.2.0)
## prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.2.0)
## processx 3.6.1 2022-06-17 [1] CRAN (R 4.2.0)
## progress 1.2.2 2019-05-16 [1] CRAN (R 4.2.0)
## ps 1.7.1 2022-06-18 [1] CRAN (R 4.2.0)
## purrr 0.3.4 2020-04-17 [1] CRAN (R 4.2.0)
## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
## R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
## R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0)
## R6 2.5.1 2021-08-19 [1] CRAN (R 4.2.0)
## rappdirs 0.3.3 2021-01-31 [1] CRAN (R 4.2.0)
## Rcpp 1.0.8.3 2022-03-17 [1] CRAN (R 4.2.0)
## RCurl 1.98-1.7 2022-06-09 [1] CRAN (R 4.2.0)
## readr 2.1.2 2022-01-30 [1] CRAN (R 4.2.0)
## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
## rlang 1.0.3 2022-06-27 [1] CRAN (R 4.2.0)
## rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0)
## rprojroot 2.0.3 2022-04-02 [1] CRAN (R 4.2.0)
## RSQLite 2.2.14 2022-05-07 [1] CRAN (R 4.2.0)
## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0)
## rvest 1.0.2 2021-10-16 [1] CRAN (R 4.2.0)
## S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
## sass 0.4.1 2022-03-23 [1] CRAN (R 4.2.0)
## scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
## stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0)
## SummarizedExperiment 1.26.1 2022-05-01 [1] Bioconductor
## VP TCGAbiolinks * 2.25.2 2022-06-16 [?] Bioconductor (on disk 2.24.3)
## TCGAbiolinksGUI.data 1.16.0 2022-04-28 [1] Bioconductor
## testthat * 3.1.4 2022-04-26 [1] CRAN (R 4.2.0)
## tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0)
## tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.0)
## tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
## tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
## vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
## vroom 1.5.7 2021-11-30 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0)
## XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0)
## xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
## XVector 0.36.0 2022-04-26 [1] Bioconductor
## yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## V ── Loaded and on-disk version mismatch.
## P ── Loaded and on-disk path mismatch.
##
## ──────────────────────────────────────────────────────────────────────────────