trans_location: Find translocations

Description Usage Arguments Value Examples

View source: R/process.R

Description

Synteny blocks and CNVs are combined to detect matching translocations.

Usage

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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

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## 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 14, 2017, 3 p.m.