plot_trans_locations: Plot translocations

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

Description

Plots translocations for whole population.

Usage

plot_trans_locations(dat, sb = NULL)

Arguments

dat	List object, containing at least two matrices "intensity" and "theta" and two vectors "chr" and "pos".
sb	synteny block object

Examples

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)
plot_trans_locations(dat, sb = synteny_blocks$blocks)
}

Example output

Loading required package: brassicaData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'brassicaData'

gsrc documentation built on May 30, 2017, 4:16 a.m.