Error in dmTest() from DRIMSeq package - tuQTL
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@iaradsouza1-23569
Last seen 20 months ago
Brazil

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 • 974 views
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@gosia-nowicka-9493
Last seen 8 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

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