Description
Validate and Convert Mutational Impacts Using Standard Genomic Dictionaries.
Description
Check concordance of a vector of mutation impacts with standard dictionaries such as Sequence Ontology (SO) <http://www.sequenceontology.org/>, Mutation Annotation Format (MAF) <https://docs.gdc.cancer.gov/Encyclopedia/pages/Mutation_Annotation_Format_TCGAv2/> or Prediction and Annotation of Variant Effects (PAVE) <https://github.com/hartwigmedical/hmftools/tree/master/pave>. It enables conversion between SO/PAVE and MAF terms and selection of the most severe consequence where multiple ampersand (&) delimited impacts are given.
README.md
mutationtypes 
Say you want to describe the impact of a mutation. There exists several dictionaries you could use, including
Sequence Ontology. These terms are what VEP uses
PAVE Consequences that the PAVE annotator supports (mostly a subset of SO terms but with a couple of additions to indicate when a non-obvious consequence can be found thanks to phasing)
mutationtypes makes it easy to check whether your vector of mutation types aligns to one of these dictionaries. It also simplifies translation from one dictionary to another.
Installation
Install from CRAN:
install.packages("mutationtypes")
Alternatively, you can install the development version of mutationtypes like so:
# install.packages('remotes')
remotes::install_github('selkamand/mutationtypes')
Usage
library(mutationtypes)
# Check which mutation impact dictionary you're vector is closest too
mutation_types_identify(
c(
"INTRAGENIC",
"INTRAGENIC",
"intergenic_region",
"stop_lost",
"missense_variant",
"missense_variant"
)
)
#>
#> ── Identify Class ──
#>
#> ℹ Found 4 unique mutation types in input set
#> ℹ 2/4 mutation types were valid PAVE terms
#> ℹ 4/4 mutation types were valid SO terms
#> ℹ 0/4 mutation types were valid MAF terms
#>
#> ── PAVE Mutation Types ──
#>
#> → stop_lost and missense_variant
#> [1] "SO"
# Convert sequence ontology mutation classes to MAF terms
mutation_types_convert_so_to_maf(
so_mutation_types = c(
"INTRAGENIC",
"INTRAGENIC",
"intergenic_region",
"stop_lost",
"missense_variant",
"missense_variant"
)
)
#>
#> ── Validating Input ──
#>
#> ✔ Supplied mutation types are valid so terms
#> [1] "Intron" "Intron" "IGR"
#> [4] "Nonstop_Mutation" "Missense_Mutation" "Missense_Mutation"
# Convert PAVE mutation classes to MAF terms
mutation_types_convert_pave_to_maf(
pave_mutation_types = c('upstream_gene_variant', 'phased_inframe_insertion', 'phased_missense')
)
#>
#> ── Validating Input ──
#>
#> ✔ Supplied mutation types are valid pave terms
#> [1] "5'Flank" "In_Frame_Ins" "Missense_Mutation"
# Get list of valid MAF terms
mutation_types_maf()
#> [1] "Splice_Site" "Nonsense_Mutation" "Frame_Shift_Del"
#> [4] "Frame_Shift_Ins" "In_Frame_Ins" "In_Frame_Del"
#> [7] "Missense_Mutation" "Splice_Region" "Intron"
#> [10] "Nonstop_Mutation" "Translation_Start_Site" "Silent"
#> [13] "RNA" "5'UTR" "3'UTR"
#> [16] "5'Flank" "3'Flank" "Targeted_Region"
#> [19] "IGR"
# Get list of valid SO terms
mutation_types_so()
#> [1] "transcript_ablation"
#> [2] "exon_loss_variant"
#> [3] "splice_acceptor_variant"
#> [4] "splice_donor_variant"
#> [5] "stop_gained"
#> [6] "frameshift_variant"
#> [7] "stop_lost"
#> [8] "start_lost"
#> [9] "initiator_codon_variant"
#> [10] "inframe_insertion"
#> [11] "inframe_deletion"
#> [12] "protein_altering_variant"
#> [13] "missense_variant"
#> [14] "conservative_missense_variant"
#> [15] "rare_amino_acid_variant"
#> [16] "transcript_amplification"
#> [17] "splice_region_variant"
#> [18] "splice_donor_5th_base_variant"
#> [19] "splice_donor_region_variant"
#> [20] "splice_polypyrimidine_tract_variant"
#> [21] "start_retained_variant"
#> [22] "stop_retained_variant"
#> [23] "synonymous_variant"
#> [24] "incomplete_terminal_codon_variant"
#> [25] "coding_sequence_variant"
#> [26] "mature_miRNA_variant"
#> [27] "exon_variant"
#> [28] "5_prime_UTR_variant"
#> [29] "3_prime_UTR_variant"
#> [30] "5_prime_UTR_premature_start_codon_gain_variant"
#> [31] "non_coding_transcript_exon_variant"
#> [32] "non_coding_exon_variant"
#> [33] "INTRAGENIC"
#> [34] "intragenic_variant"
#> [35] "intron_variant"
#> [36] "non_coding_transcript_variant"
#> [37] "nc_transcript_variant"
#> [38] "NMD_transcript_variant"
#> [39] "upstream_gene_variant"
#> [40] "downstream_gene_variant"
#> [41] "TFBS_ablation"
#> [42] "TFBS_amplification"
#> [43] "TF_binding_site_variant"
#> [44] "regulatory_region_ablation"
#> [45] "regulatory_region_amplification"
#> [46] "regulatory_region_variant"
#> [47] "regulatory_region"
#> [48] "feature_elongation"
#> [49] "feature_truncation"
#> [50] "intergenic_variant"
#> [51] "intergenic_region"
# Get list of valid PAVE terms
mutation_types_pave()
#> [1] "upstream_gene_variant" "intron_variant"
#> [3] "5_prime_UTR_variant" "3_prime_UTR_variant"
#> [5] "non_coding_transcript_exon_variant" "synonymous_variant"
#> [7] "phased_synonymous" "missense_variant"
#> [9] "inframe_insertion" "inframe_deletion"
#> [11] "phased_inframe_insertion" "phased_inframe_deletion"
#> [13] "phased_missense" "stop_gained"
#> [15] "frameshift_variant" "start_lost"
#> [17] "stop_lost" "splice_donor_variant"
#> [19] "splice_acceptor_variant"
# Get Palettes for MAF/SO/PAVE terms
mutation_types_maf_palette()
#> Splice_Site Nonsense_Mutation Frame_Shift_Del
#> "#33A02C" "#FB9A99" "#E31A1C"
#> Frame_Shift_Ins In_Frame_Ins In_Frame_Del
#> "#E31A1C" "#CAB2D6" "#6A3D9A"
#> Missense_Mutation Splice_Region Intron
#> "#1F78B4" "#B2DF8A" "#FDBF6F"
#> Nonstop_Mutation Translation_Start_Site Silent
#> "#A6CEE3" "#B15928" "#FDBF6F"
#> RNA 5'UTR 3'UTR
#> "#FDBF6F" "#FDBF6F" "#FDBF6F"
#> 5'Flank 3'Flank Targeted_Region
#> "#FDBF6F" "#FDBF6F" "#FDBF6F"
#> IGR
#> "#FDBF6F"