findSexGroups,LinkageGroupList,StrandStateMatrix-method {contiBAIT} | R Documentation |
Bar plot all linkage groups, with the true chromosomes of contigs coloured.
## S4 method for signature 'LinkageGroupList,StrandStateMatrix' findSexGroups(linkageGroupList, strandStateMatrix, callThreshold = 0.2)
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 |
the same LinkageGroupList entered into the function, but with potential sex chromosomes highlighted in the name attribute