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!
