Comments (1)
Hi Song,
Thanks for trying it out!
For processing such a large number of cells, there are a few steps/functions that I anticipate may take a long time. Here are a few tips on how to parallelize those steps to speed up runtime.
- Identifying potential CNVs
To identify CNVs, HoneyBADGER first uses a HMM model. Currently, you may be running the default pipeline as:
potentialCnvs <- calcGexpCnvBoundaries(gexp.norm, genes, m=0.15, chrs=paste0('chr', c(1:22)), min.traverse=3, t=1e-6, min.num.genes=3, trim=0.1, verbose=FALSE)
This can be parallelized by chromosome, though unfortunately the process is not built in:
# parallelize across 22 cores for 22 chromosomes
potentialCnvs <- mclapply(paste0('chr', c(1:22)), function(chr) {
calcGexpCnvBoundaries(gexp.norm, genes, m=0.15, chrs=chr, min.traverse=3, t=1e-6, min.num.genes=3, trim=0.1, verbose=FALSE)
}, mc.cores=22)
- Testing individual CNVs in individual cells
Again, this component can also be parallelized across your identified potential CNVs though unfortunately the parallelization is not built in. For example:
results <- mclapply(potentialCnvs$region, function(region) {
results <- calcGexpCnvProb(gexp.mats$gexp.norm, gexp.mats$genes,
mvFit, region=region, verbose=TRUE)
}, mc.cores=length(potentialCnvs$region))
Because HoneyBADGER leverages information across cells within a Bayesian framework to infer the posterior probability of CNVs within individual cells, I would not recommend parallelizing by splitting up your cells into many small groups for example.
Hope that helps,
Jean
from honeybadger.
Related Issues (20)
- lt$setGexpDev HOT 1
- Warning in setGeneFactors and error in retestIdentifiedCnvs
- Allele-mode for selecting normal cells HOT 2
- 10X + Honeybadger question HOT 2
- Error in summarizeResults HOT 3
- Error in calcGexpCnvBoundaries when running with numeric chromosome names HOT 1
- Error: subscript contains invalid names HOT 9
- read bam files HOT 4
- Filtering of identified CNVs HOT 2
- speed of running setAlleleMats step
- What is the reason for only including snps in HoneyBADGER? HOT 2
- gene filtering different in HoneyBADGER object HOT 3
- Error: Failed to install 'HoneyBADGER' from GitHub HOT 2
- Showing error when trying Getting_Started.Rmd
- no method for coercing this S4 class to a vector HOT 3
- showing NULL in the step of calcGexpCnvBoundaries - getting started tutorial HOT 12
- Applying bayesian hierarchical model in integrating analyses tutorial
- error in hb$summarizeResults
- Error in summarizeResults for the allele-based approach
- Error in calcCombCnvProb HOT 1
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from honeybadger.