search

im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
212 stars 48 forks source link

'closure error' plz help me. #42

Closed a00101 closed 4 years ago

a00101 commented 4 years ago

head(data) sampleID chr pos ref mut 1 NSLA_198 chr6 53507580 T A 2 NSLA_198 chr1 24456220 C T 3 NSLA_198 chr3 50159664 C T 4 NSLA_198 chr7 150856517 C T 5 NSLA_198 chr7 150858827 A G 6 NSLA_198 chr7 43479738 T C dndsout = dndscv(data, cv=Null, refdb = "DNDSCV/RefCDS_human_GRCh38.p12.rda") [1] Loading the environment... [2] Annotating the mutations... Note: 53 mutations removed for exceeding the limit of mutations per gene per sample (see the max_muts_per_gene_per_sample argument in dndscv) [3] Estimating global rates... [4] Running dNdSloc... [5] Running dNdScv... Error in covs[genemuts$gene_name, ] : object of type 'closure' is not subsettable In addition: Warning messages: 1: In dndscv(data, cv = Null, refdb = "DNDSCV/RefCDS_human_GRCh38.p12.rda") : Same mutations observed in different sampleIDs. Please verify that these are independent events and remove duplicates otherwise. 2: glm.fit: fitted rates numerically 0 occurred 3: glm.fit: fitted rates numerically 0 occurred

im3sanger commented 4 years ago

Hello,

Apologies for the slow response, somehow I had missed this message until now. I have never encountered this error before. From the error message that you are getting, it could be that you need to specify "cv=NULL" in upper case, instead of "cv=Null".

If the above suggestion does not solve your problem, please reopen this issue and perhaps send me a small example dataset that I could use to reproduce and correct the error.

Many thanks and sorry again for the unacceptably slow response, Inigo