Comments (2)
Hi Simona,
Thanks for your patience.
It looks like the error is stemming from this code in hb$summarizeResults
:
rgs <- cnvs[["allele-based"]][["all"]]
retest <- results[["allele-based"]]
del.loh.allele.prob <- do.call(rbind, lapply(retest, function(x) x))
vi1 <- rowSums(del.loh.allele.prob > 0.75) > min.num.cells
del.loh.allele.prob <- del.loh.allele.prob[vi1, ]
names <- apply(as.data.frame(rgs), 1, paste0, collapse = ":")
rownames(del.loh.allele.prob) <- paste0("del.loh.", names[vi1])
cnvs[["allele-based"]][["del.loh"]] <<- rgs[vi1]
summary[["allele-based"]] <<- del.loh.allele.prob
colnames(del.loh.allele.prob) <- paste0("del.loh.allele.", colnames(del.loh.allele.prob))
df <- cbind(as.data.frame(rgs), avg.del.loh.allele = rowMeans(del.loh.allele.prob), del.loh.allele.prob)
because, as you aptly noted, rgs <- cnvs[["allele-based"]][["all"]]
has 15 alterations identified. But del.loh.allele.prob
has been filtered to only the alternations affecting more than min.num.cells
with greater than 75% posterior probability. In hindsight this should probably also be modified to take a parameter to allow users to have greater stringency on the posterior probability filter.
The fastest hack-y "fix" I believe is to just set min.num.cells = 0
instead of the default = 2.
The correction would be to have:
df <- cbind(as.data.frame(rgs[vi1]), avg.del.loh.allele = rowMeans(del.loh.allele.prob), del.loh.allele.prob)
Can you please double check that the following code works for you?
rgs <- hb$cnvs[["allele-based"]][["all"]]
retest <- hb$results[["allele-based"]]
del.loh.allele.prob <- do.call(rbind, lapply(retest, function(x) x))
min.num.cells <- 2
vi1 <- rowSums(del.loh.allele.prob > 0.75) > min.num.cells
del.loh.allele.prob <- del.loh.allele.prob[vi1, ]
names <- apply(as.data.frame(rgs), 1, paste0, collapse = ":")
rownames(del.loh.allele.prob) <- paste0("del.loh.", names[vi1])
colnames(del.loh.allele.prob) <- paste0("del.loh.allele.", colnames(del.loh.allele.prob))
df <- cbind(as.data.frame(rgs[vi1]), avg.del.loh.allele = rowMeans(del.loh.allele.prob), del.loh.allele.prob)
print(df)
If it works, I can make the appropriate corrections to the repo and acknowledge you in the commit message.
Thanks,
Jean
from honeybadger.
Hi Jean,
Thanks for the reply and for the fix; the code works for me.
from honeybadger.
Related Issues (20)
- lt$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
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from honeybadger.