findSexGroups,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation

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

### 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

[Package contiBAIT version 1.10.1 Index]