setGenomicSequences: Change the underlying genomic sequences of a...
In ErasmusMC-CCBC/ProteoDisco: Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences
setGenomicSequences R Documentation
Change the underlying genomic sequences of a ProteoDiscography object.
Description
Change the underlying genomic sequences of a ProteoDiscography object.
Usage
setGenomicSequences(x, genomeSeqs)
## S4 method for signature 'ProteoDiscography'
setGenomicSequences(x, genomeSeqs)
Arguments
x
(ProteoDiscography): ProteoDiscography object.
genomeSeqs
(DNAStringSet or BSgenome): Genomic sequence of the respective genome.
Value
ProteoDiscography with updated genomic sequences.
Examples
# Import example ProteoDiscography (hg19) and re-link genomic sequences.
data('ProteoDiscographyExample.hg19', package = 'ProteoDisco')
ProteoDiscographyExample.hg19 <- setTxDb(ProteoDiscographyExample.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene)
ProteoDiscographyExample.hg19 <- setGenomicSequences(ProteoDiscographyExample.hg19, BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)
summary(ProteoDiscographyExample.hg19)
ErasmusMC-CCBC/ProteoDisco documentation built on Dec. 9, 2022, 8:41 a.m.
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| setGenomicSequences | R Documentation |
Change the underlying genomic sequences of a ProteoDiscography object.
Description
Change the underlying genomic sequences of a ProteoDiscography object.
Usage
setGenomicSequences(x, genomeSeqs) ## S4 method for signature 'ProteoDiscography' setGenomicSequences(x, genomeSeqs)
Arguments
x |
(ProteoDiscography): ProteoDiscography object. |
genomeSeqs |
(DNAStringSet or BSgenome): Genomic sequence of the respective genome. |
Value
ProteoDiscography with updated genomic sequences.
Examples
# Import example ProteoDiscography (hg19) and re-link genomic sequences.
data('ProteoDiscographyExample.hg19', package = 'ProteoDisco')
ProteoDiscographyExample.hg19 <- setTxDb(ProteoDiscographyExample.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene::TxDb.Hsapiens.UCSC.hg19.knownGene)
ProteoDiscographyExample.hg19 <- setGenomicSequences(ProteoDiscographyExample.hg19, BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19)
summary(ProteoDiscographyExample.hg19)
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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