I can get DECoN to work for one of my sets of data, but for another set I keep getting the error below during the makeCNVcalls.R step.
[1] "Processing sample: 201_S6 7/7"
Optimization of the choice of aggregate reference set, this process can take some time
Number of selected bins: 63
Now fitting the beta-binomial model on a data frame with 82 rows : this step can take a few minutes.
Now computing the likelihood for the different copy number states
Correlation between reference and tests count is 0.98512
To get meaningful result, this correlation should really be above 0.97. If this is not the case, consider the output of ExomeDepth as less reliable (i.e. most likely a high false positive rate)
Number of calls for chromosome chr7 : 1
Error in Summary.factor(45:53, na.rm = FALSE) :
‘min’ not meaningful for factors
Calls: unlist -> lapply -> FUN -> Summary.factor
Execution halted
Edit: I think the problem was my custom numbering file had numbers in the following format #.#.#
Is there any way to have the custom numbering column be string based and sort on the coordinates instead of the exon#? I was using #.#.# to try and force a stringish name to an exon where the design has multiple tiles across an exon and there are alternate exons (exon#.tile#.alt#)
alessia677
commented
3 years ago
Hi, I'm using DECoN v1.0.1 on Ubuntu 16.04
I can get DECoN to work for one of my sets of data, but for another set I keep getting the error below during the makeCNVcalls.R step.
Edit: I think the problem was my custom numbering file had numbers in the following format #.#.# Is there any way to have the custom numbering column be string based and sort on the coordinates instead of the exon#? I was using #.#.# to try and force a stringish name to an exon where the design has multiple tiles across an exon and there are alternate exons (exon#.tile#.alt#)