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Hi,
apologies for bothering you again but I have a question about the results from SMultiXcan. The software ran flawlessy with the elastic net models and correcting for heritability, but when analyzing the results file I found that there are multiple rows with the same gene_name, but with different z_mean and pvalue. When running this on my results dataframe imported into R
results %>%
count(gene_name) %>%
filter(n > 1)
I get these results:
# A tibble: 4 × 2
gene_name n
<chr> <int>
1 LINC01115 2
2 LINC01422 2
3 LYNX1 2
4 SPATA13 2
If I then look at the individual genes (i.e., SPATA13) with this code
results %>%
filter(gene_name == "SPATA13") %>%
select(gene, gene_name, z_mean, pvalue)
obtain this:
# A tibble: 2 × 4
gene gene_name z_mean pvalue
<chr> <chr> <dbl> <dbl>
1 ENSG00000182957.15 SPATA13 -0.938 0.348
2 ENSG00000228741.2 SPATA13 0.125 0.870
Since I am no expert in the field, I wanted to ask whether this is to be expected or if it is a bug in the results or in the data.
If this is an expected, which of the gene copies do i select?
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