loadIndex: loadIndex
In robinweide/tagmeppr: A computational pipeline to map tagmap-insertions

Description Usage Arguments Value Author(s) Examples

View source: R/makeIndex.R

Load a hybrid reference genome

1	loadIndex(indexPath)

indexPath

The path to the *_tagMeppRindex.fa.gz made by makeIndex.

A tagMepprIndex-object with the following slots:

index: The path to the .fa.gz of hybrid reference genome
ITR: The name of the used transposon-system or ITR.fa
TIS: A GRanges-object of all target insertion sites.
targetInsertionSite: The targetInsertionSite
insertName: The name of the transposon in the hybrid reference
seqinfo: A seqinfo object of all chromosomes in index.
NpadRange: The positions of the N-padding in the ITR-sequence.

Robin H. van der Weide, r.vd.weide@nki.nl

## Not run: 
reference_hg19_PB = makeIndex(indexPath = '/home/A.Dent/analysis42/',
                              bsgenome = BSgenome.Hsapiens.UCSC.hg19,
                              ITR = 'PiggyBac')

# stuff happens and reference_T42 is no longer loaded, so lets load it:
reference_hg19_PB = loadIndex("BSgenome.Hsapiens.UCSC.hg19_PiggyBac_tagMeppRindex.fa.gz")

## End(Not run)