missing 1.6_tfModules_asDF.Rds file

[KabitaBaral1]

Hi,

I used pySCENIC to run GRNBoost and imported the output to SCENIC using the following code:

GRNBoost_output <- read.delim("/Users/kabitabaral/Desktop/SCENIC/data/adjacencies.tsv") colnames(GRNBoost_output) <- c("TF","Target","weight") saveRDS(GRNBoost_output, file="/Users/kabitabaral/Desktop/int/1.4_GENIE3_linkList.Rds")

But, I am missing the file: 1.6_tfModules_asDF.Rds from getting generated and when I try to run the next step in SCENIC, that is:

runSCENIC_1_coexNetwork2modules(scenicOptions)

I get the following error: 14:06 Creating TF modules 75% 90% 1.534220 4.675815 [,1] nTFs 150 nTargets 1734 nGeneSets 898 nLinks 581526 Error in corrMat[tf, targets] : subscript out of bounds

Are the two issues related? the missing file and "subscript out of bounds" error?

How can I fix this error?

Thank you

[ykwee]

Hi @KabitaBaral1 ,

I have the same issue before but I'm not sure if this would help. I guess you have to use the filtered gene expression matrix to run the GRNBoost first then only import in SCENIC (I mean the same loom file to run in both GRNBoost and SCENIC).

Thanks. Dan

[KabitaBaral1]

Hi @danwee ,

I tried this but it did not fix the issue for me. Did this fix the issue for you? Thank you

[morganee261]

Hello @KabitaBaral1 and @danwee,

I am having the same issue, since my dataset is too big for GENIE3 I used the CLI and GRNBoost and I am importing the results in R to complete the SCENIC script. I am missing the same files as you and I am not sure which ones they are. @cflerin would you be able to help or point us to a tutorial ?

thanks morgane

[cflerin]

I don't usually run the analysis this way (python -> R), but the error:

Error in corrMat[tf, targets] : subscript out of bounds

makes me think that maybe a different expression matrix (or set of TFs) is being used in python GRNBoost2 vs the R steps. Otherwise, it could be that some of the steps in the R tutorial were skipped. Things are run in a slightly different order in python vs R, especially the correlation calculation, so maybe try re-running this step after loading the expression matrix and GRN output into R...

[jwg054000]

I'm also having the same issue:

Error in corrMat[tf, targets] : subscript out of bounds