gsrc (version 1.0.1)

trans_location: Find translocations

Description

Synteny blocks and CNVs are combined to detect matching translocations.

Usage

trans_location(dat, sb, min = 1L)

Arguments

dat

List object, containing at least two matrices "baf" and "rratio" and two vectors "chr" and "pos".

sb

synteny_info object

min

Integer, minimal number of markers below / above threshold.

Value

norm_data object including a CNA object.

Examples

## Not run: 
# if(require(brassicaData)){
# data("raw_napus", package = "brassicaData", envir = environment())
# dat <- intens_theta(raw_napus)
# dat <- remove_suffix(dat, "_Grn")
# dat <- geno_baf_rratio(dat, delthresh = 11)
# dat <- segm(dat)
# dat <- cnv(dat, dup = 0.03, del = -0.06)
# data("synteny_blocks", package = "brassicaData", envir = environment())
# dat <- trans_location(dat, synteny_blocks, min = 5)
# }
# ## End(Not run)