intersectXMLAnnot {hoardeR} | R Documentation |
Intersect XML object with annotation object
Description
For a annotation object this function intersects the loci of it with the output of the tableSpecies function.
Usage
intersectXMLAnnot(tabSpecies, annot, level="gene", flanking=NULL)
Arguments
tabSpecies |
The table with locations from |
annot |
The annotation object. |
level |
The level of intersection. |
flanking |
Allowed flanking space for intersection. |
Details
Function expects as an input table from tableSpecies
with the option locations=TRUE
. Further, it needs an annotation object,
as provided by the getAnnotation
function. With that it intersects then the loci on the level as specified in level
. Currently
only "gene"
is supported.
The flanking
option allows for flanking space up- and down-stream of the genes. This is especially then useful if the novel gene
candidates are in the extension of known genes (e.g. responsible for regulation or if they are novel exons.)
Value
A table with intersection loci.
Author(s)
Daniel Fischer
Examples
## Not run:
pigHits <- tableSpecies(xmls, species="Sus scrofa", locations = TRUE)
ssannot <- getAnnotation(species = "Sus scrofa", annotationFolder="/home/user/annotation")
pigInter <- list()
for(i in 1:nrow(pigHits)){
pigInter[[i]] <- intersectXMLAnnot(pigHits[i,], ssannot)
}
## End(Not run)