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

Description Usage Arguments Value Author(s) Examples

View source: R/makeIndex.R

Generate a hybrid reference genome

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makeIndex(indexPath, bsgenome = NULL, ITR = "PiggyBac",
  targetInsertionSite = "TTAA", blockSizeMult = NULL,
  BWA_path = NULL, verbose = F)

`indexPath`	A path to the folder to store the reference-files.
`bsgenome`	A BSgenome onject (default: BSgenome.Hsapiens.UCSC.hg19)
`ITR`	Can take PiggyBac (default), SleepingBeauty, or a path to a 1000xN-padded ITR.fasta.
`targetInsertionSite`	The target insertion site of your system ("TTAA" for piggyBac, "TA" for sleepingBeauty)
`blockSizeMult`	Set a blocksize multiplication factor for BWA index. If left NULL, will use calculate optimal value. Change only when absolutely needed and when you have read this thread.
`BWA_path`	A string to the complete BWA-path.
`verbose`	Do you want a more chatty function?

Resulting files stored as [indexPath]/[bsgenome]_[ITR]_tagMeppRindex.*. The .fa file will be the hybrid reference genome, while the .tis file stores all possible insertions sites.

The function also returns a tagMepprIndex-object with the following slots:

index: The path to the 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')

## End(Not run)