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

In 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

contiBAIT documentation built on Nov. 8, 2020, 5:49 p.m.