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 1.12.0 Index]