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ErasmusMC-CCBC / katdetectr

An R package for detection, characterization and visualization of kataegis.
GNU General Public License v3.0
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Error: Exponential test statistic requires positive data #1

Closed chauzej closed 1 year ago

chauzej commented 1 year ago

Hi,

We are trying to use the package katdetectr.

When starting the command line kdVCF <- detectKataegis(genomicVariants = FileX), we systematically have the following error :

Error: BiocParallel errors 1 remote errors, element index: 5 19 unevaluated and other errors first remote error: Error in multiple.meanvar.exp(data, mul.method = method, penalty, pen.value, : Exponential test statistic requires positive data

Could you please help us ?

Sincerely.

HarmenvdWerken commented 1 year ago

Dear Chauzej,

Thank you for your remark. Could you please send me the input file you are using to h.vandewerken[at]erasmusmc.nl

All the best, Harmen

daanhazelaar commented 1 year ago

Dear @chauzej

Thanks for opening this issue!

I have updated katdetectr which should fix your problem. Make sure that you specify the correct reference genome used for the variant calling. You can specify this using the refSeq argument in detectKataegis().

Please see the code below:

# download the latest version of katdetectr from github
devtools::install_git(url = "https://github.com/ErasmusMC-CCBC/katdetectr")

# load and attach katdetectr
library("katdetectr")

# detect kataegis
kd <- detectKataegis(genomicVariants = "path/to/file.vcf", refSeq = "hg38")

# visualize in a rainfall plot
rainfallPlot(kd)

Please let me know if you experience any other problems!

Kind regards, Daan Hazelaar