txdbToGRangesList: Convert TxDb object to GRangesList
In mfansler/txcutr: Transcriptome CUTteR
Description
Usage
Arguments
Value
Examples
Description
Convert TxDb object to GRangesList
Usage
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txdbToGRangesList(
txdb,
geneCols = c("gene_id"),
transcriptCols = c("gene_id", "tx_name"),
exonCols = c("gene_id", "tx_name", "exon_id", "exon_rank")
)
Arguments
txdb
a TxDb object
geneCols
names of columns to include in the genes ranges
transcriptCols
names of columns to include in the transcripts ranges
exonCols
names of columns to include in the exons ranges
Value
a GRangesList object with entries c(genes, transcripts, exons)
Examples
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library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
grl <- txdbToGRangesList(txdb)
grl
mfansler/txcutr documentation built on Dec. 21, 2021, 4:59 p.m.
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Description Usage Arguments Value Examples
Description
Convert TxDb object to GRangesList
Usage
1 2 3 4 5 6 | txdbToGRangesList(
txdb,
geneCols = c("gene_id"),
transcriptCols = c("gene_id", "tx_name"),
exonCols = c("gene_id", "tx_name", "exon_id", "exon_rank")
)
|
Arguments
txdb |
a |
geneCols |
names of columns to include in the |
transcriptCols |
names of columns to include in the |
exonCols |
names of columns to include in the |
Value
a GRangesList object with entries c(genes, transcripts, exons)
Examples
1 2 3 4 5 6 7 | library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
## load annotation
txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
grl <- txdbToGRangesList(txdb)
grl
|
R Package Documentation
Browse R Packages
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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