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Wedge-lab / dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours
GNU Affero General Public License v3.0
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Error in chromosome[, s] <- list_of_tables[[s]][, Chromosome] : number of items to replace is not a multiple of replacement length #9

Closed ardydavari closed 3 years ago

ardydavari commented 3 years ago

I used the preproc_pipeline_caveman.R to generate the allDirichletProcessInfo.txt files for my samples. And then tried running these samples.

I obtained this error: [1] "Loading data..." Error in chromosome[, s] <- list_of_tables[[s]][, Chromosome] : number of items to replace is not a multiple of replacement length Calls: RunDP -> load.data -> load.data.inner Execution halted

I investigated my input data little more closer and noticed the following discrepancy:

The example data has these columns:

chr end WT.count mut.count subclonal.CN mutation.copy.number subclonal.fraction no.chrs.bearing.mut phase

Whereas the data that was generated using preproc_pipeline_caveman.R from dpclust3p are: chr start end WT.count mut.count subclonal.CN nMaj1 nMin1 frac1 nMaj2 nMin2 frac2 phase mutation.copy.number subclonal.fraction no.chrs.bearing.mut

Does this input data need to be modified to match the example? Thank you

ardydavari commented 3 years ago

I edited the input data to match the example, and I am still getting this error:

[1] "Loading data..." Error in chromosome[, s] <- list_of_tables[[s]][, Chromosome] : number of items to replace is not a multiple of replacement length Calls: RunDP -> load.data -> load.data.inner Execution halted

ardydavari commented 3 years ago

I figured out that this error was because the mutations that were identified by dpclust3p were not available in all samples. Removing the non-overlapping mutations seems to have corrected this error.