clonalCompare chain argument

[ncborcherding]

Per #475

Selecting an individual TRB chain in clonalCompare creates an error:

combined.TCR <- combineTCR(contig_list, 
                           samples = c("P17B", "P17L", "P18B", "P18L", 
                                       "P19B","P19L", "P20B", "P20L"))
   
clonalCompare(combined.TCR,
              chain = "TRB")     

Error: chain is not in c("both", "TRA", "TRG", "IGH", "IGL")

[ncborcherding]

There was an assert that statement that in did not include all of the chains - now fixed:

is.string(chain), chain %in% c("both", "TRA", "TRB", "TRG", "TRD", "IGH", "IGL")

Here is the updated example:

combined.TCR <- combineTCR(contig_list, 
                           samples = c("P17B", "P17L", "P18B", "P18L", 
                                       "P19B","P19L", "P20B", "P20L"))
   
clonalCompare(combined.TCR,
              chain = "TRB")  

clonalCompare(combined.TCR[1:2],
                         chain = "TRB", 
                         top.clones = 10)  

[airabiotenor]

Hi @ncborcherding is it possible to add "IGK" as well? Or is there a reason it is excluded as a chain option?