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I think I discovered a bug when loading GWAS sumstats. Some of my sumstats have the rsid as the last column in the file. This resulted in seemingly correct loading of the data. PascalX proceeds to scoring the genes, but the scoring results in 0 genes scored.
After some trial and error, I realized that simply putting the rsid column not as the last one solved the issue.
As a minimal example, this was the format of the .tsv that worked:
rsid Effect P-value
rs7899632 -0.0246 0.0958
This is the same file, with rsid as the last column, that doesn't work:
Effect P-value rsid
-0.0246 0.0958 rs7899632
The text was updated successfully, but these errors were encountered:
Hi,
I think I discovered a bug when loading GWAS sumstats. Some of my sumstats have the
rsid
as the last column in the file. This resulted in seemingly correct loading of the data. PascalX proceeds to scoring the genes, but the scoring results in 0 genes scored.After some trial and error, I realized that simply putting the
rsid
column not as the last one solved the issue.As a minimal example, this was the format of the
.tsv
that worked:This is the same file, with rsid as the last column, that doesn't work:
The text was updated successfully, but these errors were encountered: