drugInteractions: Drug-Gene Interactions
In maftools: Summarize, Analyze and Visualize MAF Files
Description
Usage
Arguments
Details
References
Examples
View source: R/drugInteractions.R
Description
Checks for drug-gene interactions and druggable categories
Usage
1
2
3
4
5
6
7
8
drugInteractions(
maf,
top = 20,
genes = NULL,
plotType = "bar",
drugs = FALSE,
fontSize = 0.8
)
Arguments
maf
an MAF object generated by read.maf
top
Top number genes to check for. Default 20
genes
Manually specify gene list
plotType
Can be bar, pie Default bar plot.
drugs
Check for known/reported drugs. Default FALSE
fontSize
Default 0.8
Details
This function takes a list of genes and checks for known/reported drug-gene interactions or Druggable categories.
All gene-drug interactions and drug claims are compiled from Drug Gene Interaction Databse. See reference for details and cite it if you use this function.
References
Griffith, M., Griffith, O. L., Coffman, A. C., Weible, J. V., McMichael, J. F., Spies, N. C., et. al,. 2013. DGIdb - Mining the druggable genome. Nature Methods.
Examples
1
2
3
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
drugInteractions(maf = laml)
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.608s elapsed (0.444s cpu)
Gene gene_long_name
1: STAG2 STROMAL ANTIGEN 2
2: STAG2 STROMAL ANTIGEN 2
3: WT1 WILMS TUMOR 1
4: WT1 WILMS TUMOR 1
5: TP53 TUMOR PROTEIN P53
6: TP53 TUMOR PROTEIN P53
7: TP53 TUMOR PROTEIN P53
8: TP53 TUMOR PROTEIN P53
9: TP53 TUMOR PROTEIN P53
10: TP53 TUMOR PROTEIN P53
11: TP53 TUMOR PROTEIN P53
12: TP53 TUMOR PROTEIN P53
13: TP53 TUMOR PROTEIN P53
14: U2AF1 U2 SMALL NUCLEAR RNA AUXILIARY FACTOR 1
15: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
16: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
17: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
18: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
19: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
20: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
21: IDH1 ISOCITRATE DEHYDROGENASE (NADP(+)) 1, CYTOSOLIC
22: TET2 TET METHYLCYTOSINE DIOXYGENASE 2
23: TET2 TET METHYLCYTOSINE DIOXYGENASE 2
24: TTN TITIN
25: TTN TITIN
26: TTN TITIN
27: TTN TITIN
28: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
29: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
30: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
31: NPM1 NUCLEOPHOSMIN 1
32: NPM1 NUCLEOPHOSMIN 1
33: NPM1 NUCLEOPHOSMIN 1
34: NPM1 NUCLEOPHOSMIN 1
35: NPM1 NUCLEOPHOSMIN 1
36: NPM1 NUCLEOPHOSMIN 1
37: NPM1 NUCLEOPHOSMIN 1
38: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
39: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
40: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
41: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
42: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
43: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
44: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
45: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
46: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
47: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
48: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
49: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
50: KRAS KRAS PROTO-ONCOGENE, GTPASE
51: KRAS KRAS PROTO-ONCOGENE, GTPASE
52: KRAS KRAS PROTO-ONCOGENE, GTPASE
53: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
54: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
55: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
56: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
57: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
58: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
59: NRAS NRAS PROTO-ONCOGENE, GTPASE
60: IDH2 ISOCITRATE DEHYDROGENASE (NADP(+)) 2, MITOCHONDRIAL
61: FLT3 FMS RELATED TYROSINE KINASE 3
62: FLT3 FMS RELATED TYROSINE KINASE 3
63: FLT3 FMS RELATED TYROSINE KINASE 3
64: FLT3 FMS RELATED TYROSINE KINASE 3
65: FLT3 FMS RELATED TYROSINE KINASE 3
66: FLT3 FMS RELATED TYROSINE KINASE 3
67: SMC1A STRUCTURAL MAINTENANCE OF CHROMOSOMES 1A
68: SMC1A STRUCTURAL MAINTENANCE OF CHROMOSOMES 1A
69: RUNX1 RUNT RELATED TRANSCRIPTION FACTOR 1
Gene gene_long_name
category_sources
1: FoundationOneGenes,MskImpact
2: GO
3: MskImpact,FoundationOneGenes
4: HingoraniCasas
5: HingoraniCasas,RussLampel,HopkinsGroom
6: GO
7: GO
8: GO
9: GO
10: GO
11: GO
12: GO
13: FoundationOneGenes,MskImpact,CarisMolecularIntelligence
14: MskImpact
15: GO
16: GO
17: GO
18: GO,HopkinsGroom,dGene
19: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
20: HopkinsGroom,RussLampel,HingoraniCasas,dGene
21: CarisMolecularIntelligence,FoundationOneGenes,MskImpact
22: GO
23: MskImpact,FoundationOneGenes
24: HingoraniCasas,dGene,HopkinsGroom
25: dGene,GO,GuideToPharmacologyGenes
26: GO,GuideToPharmacologyGenes,HopkinsGroom
27: GO
28: MskImpact,FoundationOneGenes
29: GO
30: HingoraniCasas
31: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
32: HingoraniCasas
33: GO
34: GO
35: GO
36: GO
37: GO
38: GO
39: GO
40: HingoraniCasas
41: GO
42: GO,GuideToPharmacologyGenes,dGene
43: GO
44: GO,HopkinsGroom,GuideToPharmacologyGenes,BaderLabGenes
45: GO
46: GO
47: GO
48: MskImpact,FoundationOneGenes,CarisMolecularIntelligence
49: HingoraniCasas,HopkinsGroom,dGene,RussLampel
50: GO
51: GO
52: FoundationOneGenes,MskImpact,CarisMolecularIntelligence
53: GO
54: GO
55: GO
56: GO
57: GO
58: FoundationOneGenes
59: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
60: CarisMolecularIntelligence,FoundationOneGenes,MskImpact
61: CarisMolecularIntelligence,MskImpact,FoundationOneGenes
62: dGene,GO,GuideToPharmacologyGenes
63: dGene,RussLampel,HopkinsGroom,HingoraniCasas
64: HopkinsGroom,GO,GuideToPharmacologyGenes
65: GO
66: GO
67: GO
68: GO
69: MskImpact,FoundationOneGenes
category_sources
category
1: CLINICALLY ACTIONABLE
2: TUMOR SUPPRESSOR
3: CLINICALLY ACTIONABLE
4: DRUGGABLE GENOME
5: DRUGGABLE GENOME
6: TUMOR SUPPRESSOR
7: TRANSCRIPTION FACTOR BINDING
8: RNA DIRECTED DNA POLYMERASE
9: DNA REPAIR
10: HISTONE MODIFICATION
11: DRUG RESISTANCE
12: TRANSCRIPTION FACTOR COMPLEX
13: CLINICALLY ACTIONABLE
14: CLINICALLY ACTIONABLE
15: TUMOR SUPPRESSOR
16: SERINE THREONINE KINASE
17: KINASE
18: PROTEIN PHOSPHATASE
19: CLINICALLY ACTIONABLE
20: DRUGGABLE GENOME
21: CLINICALLY ACTIONABLE
22: HISTONE MODIFICATION
23: CLINICALLY ACTIONABLE
24: DRUGGABLE GENOME
25: SERINE THREONINE KINASE
26: KINASE
27: TYROSINE KINASE
28: CLINICALLY ACTIONABLE
29: DRUG RESISTANCE
30: DRUGGABLE GENOME
31: CLINICALLY ACTIONABLE
32: DRUGGABLE GENOME
33: TUMOR SUPPRESSOR
34: TRANSCRIPTION FACTOR BINDING
35: DNA REPAIR
36: TYROSINE KINASE
37: KINASE
38: DNA REPAIR
39: TUMOR SUPPRESSOR
40: DRUGGABLE GENOME
41: EXTERNAL SIDE OF PLASMA MEMBRANE
42: TYROSINE KINASE
43: LIPID KINASE
44: KINASE
45: PHOSPHOLIPASE
46: CELL SURFACE
47: SERINE THREONINE KINASE
48: CLINICALLY ACTIONABLE
49: DRUGGABLE GENOME
50: SERINE THREONINE KINASE
51: KINASE
52: CLINICALLY ACTIONABLE
53: KINASE
54: SERINE THREONINE KINASE
55: TRANSCRIPTION FACTOR BINDING
56: TRANSCRIPTION FACTOR COMPLEX
57: TUMOR SUPPRESSOR
58: CLINICALLY ACTIONABLE
59: CLINICALLY ACTIONABLE
60: CLINICALLY ACTIONABLE
61: CLINICALLY ACTIONABLE
62: TYROSINE KINASE
63: DRUGGABLE GENOME
64: KINASE
65: LIPID KINASE
66: SERINE THREONINE KINASE
67: TUMOR SUPPRESSOR
68: DNA REPAIR
69: CLINICALLY ACTIONABLE
category
maftools documentation built on Feb. 6, 2021, 2 a.m.
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Description Usage Arguments Details References Examples
View source: R/drugInteractions.R
Description
Checks for drug-gene interactions and druggable categories
Usage
1 2 3 4 5 6 7 8 | drugInteractions(
maf,
top = 20,
genes = NULL,
plotType = "bar",
drugs = FALSE,
fontSize = 0.8
)
|
Arguments
maf |
an |
top |
Top number genes to check for. Default 20 |
genes |
Manually specify gene list |
plotType |
Can be bar, pie Default bar plot. |
drugs |
Check for known/reported drugs. Default FALSE |
fontSize |
Default 0.8 |
Details
This function takes a list of genes and checks for known/reported drug-gene interactions or Druggable categories. All gene-drug interactions and drug claims are compiled from Drug Gene Interaction Databse. See reference for details and cite it if you use this function.
References
Griffith, M., Griffith, O. L., Coffman, A. C., Weible, J. V., McMichael, J. F., Spies, N. C., et. al,. 2013. DGIdb - Mining the druggable genome. Nature Methods.
Examples
1 2 3 | laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools")
laml <- read.maf(maf = laml.maf)
drugInteractions(maf = laml)
|
Example output
-Reading
-Validating
-Silent variants: 475
-Summarizing
-Processing clinical data
--Missing clinical data
-Finished in 0.608s elapsed (0.444s cpu)
Gene gene_long_name
1: STAG2 STROMAL ANTIGEN 2
2: STAG2 STROMAL ANTIGEN 2
3: WT1 WILMS TUMOR 1
4: WT1 WILMS TUMOR 1
5: TP53 TUMOR PROTEIN P53
6: TP53 TUMOR PROTEIN P53
7: TP53 TUMOR PROTEIN P53
8: TP53 TUMOR PROTEIN P53
9: TP53 TUMOR PROTEIN P53
10: TP53 TUMOR PROTEIN P53
11: TP53 TUMOR PROTEIN P53
12: TP53 TUMOR PROTEIN P53
13: TP53 TUMOR PROTEIN P53
14: U2AF1 U2 SMALL NUCLEAR RNA AUXILIARY FACTOR 1
15: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
16: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
17: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
18: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
19: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
20: PTPN11 PROTEIN TYROSINE PHOSPHATASE, NON-RECEPTOR TYPE 11
21: IDH1 ISOCITRATE DEHYDROGENASE (NADP(+)) 1, CYTOSOLIC
22: TET2 TET METHYLCYTOSINE DIOXYGENASE 2
23: TET2 TET METHYLCYTOSINE DIOXYGENASE 2
24: TTN TITIN
25: TTN TITIN
26: TTN TITIN
27: TTN TITIN
28: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
29: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
30: DNMT3A DNA METHYLTRANSFERASE 3 ALPHA
31: NPM1 NUCLEOPHOSMIN 1
32: NPM1 NUCLEOPHOSMIN 1
33: NPM1 NUCLEOPHOSMIN 1
34: NPM1 NUCLEOPHOSMIN 1
35: NPM1 NUCLEOPHOSMIN 1
36: NPM1 NUCLEOPHOSMIN 1
37: NPM1 NUCLEOPHOSMIN 1
38: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
39: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
40: SMC3 STRUCTURAL MAINTENANCE OF CHROMOSOMES 3
41: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
42: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
43: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
44: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
45: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
46: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
47: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
48: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
49: KIT KIT PROTO-ONCOGENE RECEPTOR TYROSINE KINASE
50: KRAS KRAS PROTO-ONCOGENE, GTPASE
51: KRAS KRAS PROTO-ONCOGENE, GTPASE
52: KRAS KRAS PROTO-ONCOGENE, GTPASE
53: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
54: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
55: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
56: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
57: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
58: CEBPA CCAAT/ENHANCER BINDING PROTEIN ALPHA
59: NRAS NRAS PROTO-ONCOGENE, GTPASE
60: IDH2 ISOCITRATE DEHYDROGENASE (NADP(+)) 2, MITOCHONDRIAL
61: FLT3 FMS RELATED TYROSINE KINASE 3
62: FLT3 FMS RELATED TYROSINE KINASE 3
63: FLT3 FMS RELATED TYROSINE KINASE 3
64: FLT3 FMS RELATED TYROSINE KINASE 3
65: FLT3 FMS RELATED TYROSINE KINASE 3
66: FLT3 FMS RELATED TYROSINE KINASE 3
67: SMC1A STRUCTURAL MAINTENANCE OF CHROMOSOMES 1A
68: SMC1A STRUCTURAL MAINTENANCE OF CHROMOSOMES 1A
69: RUNX1 RUNT RELATED TRANSCRIPTION FACTOR 1
Gene gene_long_name
category_sources
1: FoundationOneGenes,MskImpact
2: GO
3: MskImpact,FoundationOneGenes
4: HingoraniCasas
5: HingoraniCasas,RussLampel,HopkinsGroom
6: GO
7: GO
8: GO
9: GO
10: GO
11: GO
12: GO
13: FoundationOneGenes,MskImpact,CarisMolecularIntelligence
14: MskImpact
15: GO
16: GO
17: GO
18: GO,HopkinsGroom,dGene
19: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
20: HopkinsGroom,RussLampel,HingoraniCasas,dGene
21: CarisMolecularIntelligence,FoundationOneGenes,MskImpact
22: GO
23: MskImpact,FoundationOneGenes
24: HingoraniCasas,dGene,HopkinsGroom
25: dGene,GO,GuideToPharmacologyGenes
26: GO,GuideToPharmacologyGenes,HopkinsGroom
27: GO
28: MskImpact,FoundationOneGenes
29: GO
30: HingoraniCasas
31: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
32: HingoraniCasas
33: GO
34: GO
35: GO
36: GO
37: GO
38: GO
39: GO
40: HingoraniCasas
41: GO
42: GO,GuideToPharmacologyGenes,dGene
43: GO
44: GO,HopkinsGroom,GuideToPharmacologyGenes,BaderLabGenes
45: GO
46: GO
47: GO
48: MskImpact,FoundationOneGenes,CarisMolecularIntelligence
49: HingoraniCasas,HopkinsGroom,dGene,RussLampel
50: GO
51: GO
52: FoundationOneGenes,MskImpact,CarisMolecularIntelligence
53: GO
54: GO
55: GO
56: GO
57: GO
58: FoundationOneGenes
59: FoundationOneGenes,CarisMolecularIntelligence,MskImpact
60: CarisMolecularIntelligence,FoundationOneGenes,MskImpact
61: CarisMolecularIntelligence,MskImpact,FoundationOneGenes
62: dGene,GO,GuideToPharmacologyGenes
63: dGene,RussLampel,HopkinsGroom,HingoraniCasas
64: HopkinsGroom,GO,GuideToPharmacologyGenes
65: GO
66: GO
67: GO
68: GO
69: MskImpact,FoundationOneGenes
category_sources
category
1: CLINICALLY ACTIONABLE
2: TUMOR SUPPRESSOR
3: CLINICALLY ACTIONABLE
4: DRUGGABLE GENOME
5: DRUGGABLE GENOME
6: TUMOR SUPPRESSOR
7: TRANSCRIPTION FACTOR BINDING
8: RNA DIRECTED DNA POLYMERASE
9: DNA REPAIR
10: HISTONE MODIFICATION
11: DRUG RESISTANCE
12: TRANSCRIPTION FACTOR COMPLEX
13: CLINICALLY ACTIONABLE
14: CLINICALLY ACTIONABLE
15: TUMOR SUPPRESSOR
16: SERINE THREONINE KINASE
17: KINASE
18: PROTEIN PHOSPHATASE
19: CLINICALLY ACTIONABLE
20: DRUGGABLE GENOME
21: CLINICALLY ACTIONABLE
22: HISTONE MODIFICATION
23: CLINICALLY ACTIONABLE
24: DRUGGABLE GENOME
25: SERINE THREONINE KINASE
26: KINASE
27: TYROSINE KINASE
28: CLINICALLY ACTIONABLE
29: DRUG RESISTANCE
30: DRUGGABLE GENOME
31: CLINICALLY ACTIONABLE
32: DRUGGABLE GENOME
33: TUMOR SUPPRESSOR
34: TRANSCRIPTION FACTOR BINDING
35: DNA REPAIR
36: TYROSINE KINASE
37: KINASE
38: DNA REPAIR
39: TUMOR SUPPRESSOR
40: DRUGGABLE GENOME
41: EXTERNAL SIDE OF PLASMA MEMBRANE
42: TYROSINE KINASE
43: LIPID KINASE
44: KINASE
45: PHOSPHOLIPASE
46: CELL SURFACE
47: SERINE THREONINE KINASE
48: CLINICALLY ACTIONABLE
49: DRUGGABLE GENOME
50: SERINE THREONINE KINASE
51: KINASE
52: CLINICALLY ACTIONABLE
53: KINASE
54: SERINE THREONINE KINASE
55: TRANSCRIPTION FACTOR BINDING
56: TRANSCRIPTION FACTOR COMPLEX
57: TUMOR SUPPRESSOR
58: CLINICALLY ACTIONABLE
59: CLINICALLY ACTIONABLE
60: CLINICALLY ACTIONABLE
61: CLINICALLY ACTIONABLE
62: TYROSINE KINASE
63: DRUGGABLE GENOME
64: KINASE
65: LIPID KINASE
66: SERINE THREONINE KINASE
67: TUMOR SUPPRESSOR
68: DNA REPAIR
69: CLINICALLY ACTIONABLE
category
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