Error in dmTest() from DRIMSeq package - tuQTL
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Last seen 21 months ago

Hi!

I'm using the tuQTL pipeline implemented by DRIMSeq package to analyze the genotype effect over transcript usage. As described by the package vignette, I tried to mimic the objects needed: 1. a dataframe containing the genotypes (with only the biallelic sites), 2. a dataframe for samples information, 3. a dataframe for counts (here I used the scaledTPM normalization), 4. a GRange object for genes coordinates and 5. a GRange object for SNPs coordinates.

I'm testing the analysis for chromosome 1, as a way to optimize code for the rest of the genome. However, I'm getting the following error message when I perform the test with the dmTest() function:

Error in rbind(deparse.level, ...) : numbers of columns of arguments do not match

Looking at the package code in github, I believe that something is happening when this method tries to concatenate results for each SNP. (see line 257 in https://github.com/gosianow/DRIMSeq/blob/master/R/class_dmSQTLtest.R). This is just a guess but I would appreciate some help with what could be causing this error. I didn't open an issue in github because I don't know if this is caused by a bug or if it is an intrinsic error in my dataset. Thanks in advance!

DRIMSeq tuQTL • 322 views
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@gosia-nowicka-9493
Last seen 19 months ago
Basel

Thank you for reporting this issue and for a reproducible example. The bug should be fixed now. https://github.com/gosianow/DRIMSeq/issues/6