Hello, I'm getting a cryptic error that I believe is related to reading the groupFile. The groupFile is properly formatted, so I don't know who could be causing the typing error.
Here are the most recent logs producing the error:
Thank you in advance for the help
chromosome 21 model results are removed to save memory
chromosome 22 model results are removed to save memory
P-values of genetic variants with MAC <= 4 will be calculated via effecient resampling.
variance Ratio null is 0.8724423
dosageFile type is plink
allele order in the plink file is ref-first .
Reading bim file....
Reading fam file....
Setting position of samples in PLINK files....
Start TRUE
End FALSE
SKAT-O test will be performed. P-values for BURDEN and SKAT tests will also be output
is_single_in_groupTest = TRUE. Single-variant assoc tests results will be output
Start extracting marker-level information from 'groupFile' of groupFile.txt ....
indexChunk is 0
indexChunk 0
nRegions 3736
Error in bmerge(i, x, leftcols, rightcols, roll, rollends, nomatch, mult, :
Incompatible join types: x.ID (integer) and i.SNP (character)
Calls: SPAGMMATtest ... merge -> merge.data.table -> [ -> [.data.table -> bmerge
Execution halted
Note that I formatted the groupFile according to the doc and the example files, which is chr:pos:ref:alt, NOT according to the helper function, which shows chr:pos_ref/alt
I believe I found the issue (based on browsing through previous issues, such as @evatosco's response here). It looks like the variant IDs in the plink files need to be strings; mine were integers.
Hello, I'm getting a cryptic error that I believe is related to reading the groupFile. The groupFile is properly formatted, so I don't know who could be causing the typing error. Here are the most recent logs producing the error: Thank you in advance for the help
Note that I formatted the groupFile according to the doc and the example files, which is
chr:pos:ref:alt
, NOT according to the helper function, which showschr:pos_ref/alt
My command is the following: