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Hi,
I am trying to plot Cytoband labels on the ideogram.
It works if I use the default hg19 genome, but not when I use my own genome region and cytoband files.
This is my code:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'start': subscript contains invalid names
Can you please have a look what I'm doing wrong?
Will it be possible to just set the genome parameter in the plotKaryotype function to the new assembly, so I dont have to provide genome range and cytoband file?
Thanks in advance,
Paul
The text was updated successfully, but these errors were encountered:
For anyone who is facing the same issue:
The problem seems to be that I only want to plot "chr1" but I provide 'genome' and 'cytoband ' GRanges objects containing all chromosomes. The parameter chromosomes of the plotKaryotype() function seems not to work with my custom references that I provide to the function (probably some specific formatting is needed that I'm missing).
Anyways, I figured that when I subset the GRanges objects to only "chr1" it works.
Hi,
I am trying to plot Cytoband labels on the ideogram.
It works if I use the default hg19 genome, but not when I use my own genome region and cytoband files.
This is my code:
This is an excerpt from chm13v2.bed:
This is an excerpt from cytobands_chm13v2.bed:
Unfortunately, I get this error message:
Can you please have a look what I'm doing wrong?
Will it be possible to just set the
genome
parameter in theplotKaryotype
function to the new assembly, so I dont have to provide genome range and cytoband file?Thanks in advance,
Paul
The text was updated successfully, but these errors were encountered: