ProteoDiscographyExample.hg19: Example ProteoDiscography.
In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
ProteoDiscographyExample.hg19 R Documentation
Example ProteoDiscography.
Description
A ProteoDiscography object based on validated genomic variants (hg19) using existing transcript annotations (hg19).
Usage
ProteoDiscographyExample.hg19
Format
An object of class ProteoDiscography of length 1.
Details
Generated using the following commands:
# Use existing hg19 annotations.
ProteoDiscographyExample.hg19 <- ProteoDisco::generateProteoDiscography(
TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene,
genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19
)
# Add mutations from hg19 validation set.
ProteoDiscographyExample.hg19 <- ProteoDisco::importGenomicVariants(
ProteoDiscography = ProteoDiscographyExample.hg19,
files = system.file('extdata', 'validationSet_hg19.vcf', package = 'ProteoDisco'),
samplenames = 'Validation Set (GRCh37)',
threads = 1
)
# Incorporate genomic mutations.
ProteoDiscographyExample.hg19 <- ProteoDisco::incorporateGenomicVariants(
ProteoDiscography = ProteoDiscographyExample.hg19,
aggregateSamples = FALSE,
aggregateWithinExon = TRUE,
aggregateWithinTranscript = FALSE,
ignoreOverlappingMutations = TRUE,
threads = 1
)
Source
ErasmusMC-CCBC/ProteoDisco documentation built on Dec. 9, 2022, 8:41 a.m.
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| ProteoDiscographyExample.hg19 | R Documentation |
Example ProteoDiscography.
Description
A ProteoDiscography object based on validated genomic variants (hg19) using existing transcript annotations (hg19).
Usage
ProteoDiscographyExample.hg19
Format
An object of class ProteoDiscography of length 1.
Details
Generated using the following commands: # Use existing hg19 annotations. ProteoDiscographyExample.hg19 <- ProteoDisco::generateProteoDiscography( TxDb = TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene, genomeSeqs = BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19 )
# Add mutations from hg19 validation set. ProteoDiscographyExample.hg19 <- ProteoDisco::importGenomicVariants( ProteoDiscography = ProteoDiscographyExample.hg19, files = system.file('extdata', 'validationSet_hg19.vcf', package = 'ProteoDisco'), samplenames = 'Validation Set (GRCh37)', threads = 1 )
# Incorporate genomic mutations. ProteoDiscographyExample.hg19 <- ProteoDisco::incorporateGenomicVariants( ProteoDiscography = ProteoDiscographyExample.hg19, aggregateSamples = FALSE, aggregateWithinExon = TRUE, aggregateWithinTranscript = FALSE, ignoreOverlappingMutations = TRUE, threads = 1 )
Source
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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