trans_location: Find translocations

In grafab/gsrc: Genome Structure Rearrangement Calling in Genomes with High Synteny

Description

Synteny blocks and CNVs are combined to detect matching translocations.

Usage

trans_location(dat, sb, min1 = 1L, min2 = min1, maxdiff = 4L)

Arguments

dat	List object, containing at least two matrices "baf" and "rratio" and two vectors "chr" and "pos".
sb	synteny_info object
min1	Integer, minimal number of markers below / above threshold in the first genome.
min2	Integer, minimal number of markers below / above threshold in the second genome.
maxdiff	Integer, maximal difference of marker numbers between corresponding deletion and duplication. Avoids false positives in case unique events of unequal size are in synteny by chance.

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, min1 = 5, min2 = 5, maxdiff = 20)
}

## End(Not run)

grafab/gsrc documentation built on May 17, 2019, 8:18 a.m.