HoneyBADGER

HoneyBADGER copied to clipboard

Error in calcCombCnvProb

1

Hi Prof. Fan, Thank you for your development of HoneyBADGER! I tried `hb$retestIdentifiedCnvs(retestBoundGenes=TRUE, retestBoundSnps=TRUE, verbose=FALSE)` and get the error: **Error in as.vector(x) : no method for coercing this S4 class...

Rongtingting

Dear prof. Fan, I was trying the 'getting started' tutorial for your HoneyBADGER package, but I am running into an error after retesting the CNVs identified by the allele-based approach....

myrthesmit

Hi I am running the HoneyBADGER (https://github.com/JEFworks-Lab/HoneyBADGER/blob/master/docs/Getting_Started.md) on simply test data and its not working. It should at least work at test data but giving error at hb$summarizeResults >> results

UmairSeemab

no method for coercing this S4 class to a vector

3

Hi Dr. Fan, Thank you so much for making this tool available. While running HoneyBADGER with my own .bam file and the reference provided, I ran into this error: Error...

Joanne-PYL

Hi Dr. Fan, Thank you for developing this useful tool. I am really new to R language. It showed error when I ran the line "hb$setGexpMats(gexp, ref, mart.obj, filter=FALSE, scale=FALSE,...

Joanne-PYL

gene filtering different in HoneyBADGER object

3

Hi, I have just installed HoneyBADGER, planning to use it for sc 10X analysis. I am seeing radically different filtering of genes between `gexp.mats hb hb$setGexpMats( as.matrix(gexpOI), as.matrix(gexpRef), mart.obj, +...

JocelynSP

Error: subscript contains invalid names

9

 What's wrong when I run the calcGexpCnvBoundaries using example data like https://jef.works/HoneyBADGER/Getting_Started.html?

suyanxun

Filtering of identified CNVs

2

Hi, I've been using your tool to identify CNVs in 10x Genomics scRNA-seq data. However, I have one question regarding the filtering of identified CNVs. When I run the calcAlleleCnvProb...

Josephinedh

Hi, thank you for providing such a useful tool. My dataset has ~9k cells and I use all ~60k SNPs provided from HoneyBADGER package (ExAC database) to run `setAlleleMats`. I...

lixin4306ren

Error in calcGexpCnvBoundaries when running with numeric chromosome names

1

Hello, I am testing the Honeybadger package and we have mapping to an assembly that has chromosome names without the "chr" so I modified `setGexpMats` to not add on "chr"...

asabjorklund