Error in called.segobj.list[[i]] : subscript out of bounds

ShixiangWang / DoAbsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

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Error in called.segobj.list[[i]] : subscript out of bounds #13

Closed chenhd9 closed 4 years ago

chenhd9 commented 4 years ago

I run it with maf and seg file. It worked well before "Absolute summarize". Could you give me some help?

ShixiangWang commented 4 years ago

The error comes from the following code

https://github.com/ShixiangWang/DoAbsolute/blob/2b49298e967279388fcef3d4fa81db9282a25886/R/DoAbsolute.R#L417-L429

Could you check you temp directory

And see if you can find the two files?

chenhd9 commented 4 years ago

yes.

ShixiangWang commented 4 years ago

That's strange, the problem should come from ABSOLUTE package code, please zip the two files and send to me by email w_shixiang@163.com, and I will test it.

ShixiangWang commented 4 years ago

@chenhd9 Yes, you are right. I can reproduce your error, and this is caused by your low purity sample.

For ABSOLUTE, it will only review the samples with call status is called.

Therefore, the program cannot find any results with called status, and got a zero element list.

You should input more samples when use DoAbsolute.

chenhd9 commented 4 years ago

wow~Thank you for your patience. I merge all the sample and it worked!