select.probewise {exonmap}R Documentation

Filtering of lists of probesets

Description

Selects or removes probeset from a probeset list based on their specificity to the genome.

Usage

    exclude.probewise(X,filter=c("exonic","intronic","intergenic","multitarget"), mt.level=1, debug=0) 
    select.probewise(X,filter=c("exonic","intronic","intergenic","multitarget"), mt.level=1, debug=0) 
    probesets.in.eset(X,data)

Arguments

X Probeset list
filter Type of the filter to be applied: 'exonic' probesets that match only exons, 'intronic' probesets that match only introns, 'multitarget', probesets that hit in more than one place, 'intergenic' - probesets that match only regions between genes, 'nulltarget', probesets that match nowhere
mt.level multi-target score to filter by
debug Output debug information. Gets more verbose with higher numbers. 0 supresses debug data.
data An ExpressionSet object

Details

Value

Vector of probeset names after filtering. probesets.in.eset returns only those probesets in the list that are defined in the ExpressionSet.

Author(s)

Michal Okoniewski

References

http://bioinformatics.picr.man.ac.uk/

See Also

probeset.stats

Examples

 
  ## Not run: 
    probesets <- gene.to.probeset("ENSG00000005893"); 
    exonics   <- select.probewise(probesets, filter="exonic")
    intronics <-  select.probewise(probesets, filter="intronic")   
  
## End(Not run)

[Package exonmap version 1.0.07 Index]