load_species_anno_db: Load species specific 'AnnotationDb'
In SeedMatchR: Find Matches to Canonical SiRNA Seeds in Genomic Features
View source: R/load_species_anno_db.R
load_species_anno_db R Documentation
Load species specific AnnotationDb
Description
Use AnnotationHub to load species-specific GTF and 2bit DNA
sequences. This function currently works for human, rat, and mouse.
The function will return:
-
$gtf: A GRanges object containing the GTF information
-
$tx.db: A tx.db object made from the GTF
-
$dna: The 2bit DNA sequence as a DNAStringSet
Usage
load_species_anno_db(species.name, remove.na.rows = TRUE)
Arguments
species.name
Species name. Options: human, rat, mouse
remove.na.rows
Remove rows with NA in the gene_id column
Value
Species specific AnnotationDb
Examples
anno.db = load_species_anno_db("human")
SeedMatchR documentation built on Oct. 25, 2023, 1:08 a.m.
R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
View source: R/load_species_anno_db.R
| load_species_anno_db | R Documentation |
Load species specific AnnotationDb
Description
Use AnnotationHub to load species-specific GTF and 2bit DNA
sequences. This function currently works for human, rat, and mouse.
The function will return:
-
$gtf: AGRangesobject containing the GTF information -
$tx.db: Atx.dbobject made from the GTF -
$dna: The 2bit DNA sequence as aDNAStringSet
Usage
load_species_anno_db(species.name, remove.na.rows = TRUE)
Arguments
species.name |
Species name. Options: human, rat, mouse |
remove.na.rows |
Remove rows with NA in the gene_id column |
Value
Species specific AnnotationDb
Examples
anno.db = load_species_anno_db("human")
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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