findSexGroups-LinkageGroupList-StrandStateMatrix-method: Bar plot all linkage groups, with the true chromosomes of...

In oneillkza/ContiBAIT: Improves Early Build Genome Assemblies using Strand-Seq Data

Description

Bar plot all linkage groups, with the true chromosomes of contigs coloured.

Usage

## S4 method for signature 'LinkageGroupList,StrandStateMatrix'
findSexGroups(linkageGroupList,
  strandStateMatrix, callThreshold = 0.2)

Arguments

linkageGroupList	a LinkageGroupList object as generated by clusterContigs
strandStateMatrix	a StrandStateMatrix object as generated by preprocessStrandTable
callThreshold	a value between 0 and 1 to threshold the proportion of libraries in which scaffolds are heterozygous (ie unlikely to be a monosome sex chromosome). Default value is 0.2

Value

the same LinkageGroupList entered into the function, but with potential sex chromosomes highlighted in the name attribute

oneillkza/ContiBAIT documentation built on June 1, 2020, 5:49 a.m.