intersectXMLAnnot: Intersect XML object with annotation object

In fischuu/hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

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 tableSpecies.
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)

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.