| Title: | Validate and Convert Mutational Impacts Using Standard Genomic Dictionaries |
| Version: | 0.0.1 |
| 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. |
| License: | LGPL (≥ 3) |
| Encoding: | UTF-8 |
| RoxygenNote: | 7.2.3 |
| Imports: | assertions, cli, data.table, stats, utils |
| Suggests: | covr, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| URL: | https://github.com/selkamand/mutationtypes |
| BugReports: | https://github.com/selkamand/mutationtypes/issues |
| NeedsCompilation: | no |
| Packaged: | 2023-12-14 09:17:33 UTC; selkamand |
| Author: | Sam El-Kamand 
[aut, cre],
Children's Cancer Institute Australia [cph] |
| Maintainer: | Sam El-Kamand <sam.elkamand@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2023-12-14 16:10:05 UTC |
mutationtypes: 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.
Author(s)
Maintainer: Sam El-Kamand sam.elkamand@gmail.com (ORCID)
Other contributors:
Children's Cancer Institute Australia [copyright holder]
See Also
Useful links:
Report bugs at https://github.com/selkamand/mutationtypes/issues
Convert PAVE Mutation Types to MAF
Description
Convert PAVE Mutation Types to MAF
Usage
mutation_types_convert_pave_to_maf(
pave_mutation_types,
variant_type = NULL,
split_on_ampersand = TRUE,
missing_to_silent = FALSE,
verbose = TRUE
)
Arguments
pave_mutation_types |
a vector of PAVE terms you want to convert to MAF variant classifications (character) |
variant_type |
a vector describing each mutations type. Valid elements include: "SNP", "DNP", "TNP", "ONP", "DEL", "INS". Used to map frameshift_variant to more specific MAF columns (character) |
split_on_ampersand |
should '&' separated PAVE terms be automatically converted to single PAVE terms based on highest severity? (flag) |
missing_to_silent |
should missing (NA) or empty (”) mutation types be converted to 'Silent' mutations? |
verbose |
verbose (flag) |
Value
matched MAF variant classification terms (character)
Examples
mutation_types_convert_pave_to_maf(
c('upstream_gene_variant', 'stop_lost', 'splice_acceptor_variant')
)
Convert SO Mutation Types to MAF
Description
Convert SO Mutation Types to MAF
Usage
mutation_types_convert_so_to_maf(
so_mutation_types,
variant_type = NULL,
inframe = NULL,
split_on_ampersand = TRUE,
missing_to_silent = FALSE,
verbose = TRUE
)
Arguments
so_mutation_types |
a vector of SO terms you want to convert to MAF variant classifications (character) |
variant_type |
a vector describing each mutations type. Valid elements include: "SNP", "DNP", "TNP", "ONP", "DEL", "INS". Used to map frameshift_variant to more specific MAF columns (character) |
inframe |
is the mutation inframe? (logical). Used to map protein_altering_variant to valid MAF columns |
split_on_ampersand |
should '&' separated SO terms be automatically converted to single SO terms based on highest severity? (flag) |
missing_to_silent |
should missing (NA) or empty (”) mutation types be converted to 'Silent' mutations? |
verbose |
verbose (flag) |
Value
matched MAF variant classification terms (character)
Examples
mutation_types_convert_so_to_maf(c('INTRAGENIC', 'INTRAGENIC', 'intergenic_region'))
Identify Mutation Dictionary Used
Description
Looks at variant consequence terms and guesses what mutation dictionary was used. SO and PAVE dictionaries overlap, meaning an observed set of terms can perfectly match both ontologies. If this happens, we assume they are SO terms.
Usage
mutation_types_identify(
mutation_types,
split_on_ampersand = TRUE,
verbose = TRUE,
ignore_missing = FALSE
)
Arguments
mutation_types |
mutation types to test (character) |
split_on_ampersand |
split mutation types in a single string separated by ampersand (&) into 2 distinct mutation type columns (flag) |
verbose |
verbose (flag) |
ignore_missing |
should we ignore missing (NA) or empty (”) mutation_types when identifying a classification scheme (flag) |
Value
one of c('SO', 'MAF', 'UNKNOWN'). Will return 'UNKNOWN' unless ALL mutation types fit with one of the supported dictionaries
Examples
mutation_types_identify(c('bob', 'billy', 'missense_variant'))
Dictionary of MAF terms
Description
Dictionary of MAF terms
Usage
mutation_types_maf()
Value
valid MAF terms (character)
Examples
mutation_types_maf()
Palettes: MAF
Description
Palettes: MAF
Usage
mutation_types_maf_palette()
Value
named vector. Names are MAF terms. Values are colors
Examples
mutation_types_maf_palette()
Dictionary of PAVE terms
Description
PAVE is a newer annotation software that supports annotaiton of mainly just a subset of SO terms, but with a couple of important additions to indicate when a non-obvious consequence can be found thanks to phasing.
Usage
mutation_types_pave()
Value
valid PAVE terms (character)
Examples
mutation_types_pave()
Palettes: PAVE
Description
Palettes: PAVE
Usage
mutation_types_pave_palette()
Value
named vector. Names are PAVE terms. Values are colors
Examples
mutation_types_pave_palette()
Dictionary of So terms
Description
Dictionary of So terms
Usage
mutation_types_so()
Value
valid SO terms (character)
Examples
mutation_types_so()
Palettes: SO
Description
Palettes: SO
Usage
mutation_types_so_palette()
Value
named vector. Names are SO terms. Values are colors
Examples
mutation_types_so_palette()
Select the most severe consequence (PAVE)
Description
Take a character vector which may contain multiple PAVE mutation types separated by '&' And choose only the most severe consequence
Usage
select_most_severe_consequence_pave(
pave_mutation_types,
missing_is_valid = FALSE
)
Arguments
pave_mutation_types |
a character vector of PAVE terms, where multiple pave_mutation_types per field are & delimited, and you want to choose the most severe consequence . |
missing_is_valid |
should NA values be considered valid mutation classes or should they throw an error? (flag) |
Value
the most severe consequence for each element in pave_mutation_types
Examples
select_most_severe_consequence_pave(
c(
"upstream_gene_variant&phased_synonymous&5_prime_UTR_variant",
"missense_variant&frameshift_variant"
)
)
#> Result:
#> c("phased_synonymous", "frameshift_variant")
Select the most severe consequence (SO)
Description
Take a character vector which may contain multiple so mutation types separated by '&' And choose only the most severe consequence
Usage
select_most_severe_consequence_so(so_mutation_types, missing_is_valid = FALSE)
Arguments
so_mutation_types |
a character vector of SO terms, where multiple so_mutation_types per field are & delimited, and you want to choose the most severe consequence . |
missing_is_valid |
should NA values be considered valid mutation classes or should they throw an error? (flag) |
Value
the most severe consequence for each element in so_mutation_types
Examples
select_most_severe_consequence_so(
c(
"intergenic_variant&feature_truncation&splice_acceptor_variant",
"initiator_codon_variant&inframe_insertion"
)
)
#> Result:
#> c("splice_acceptor_variant", "initiator_codon_variant")