Closed charlotteboys closed 2 years ago
Hi @charlotteboys, thanks for posting the error. Yes, this was a known bug in version 2.0.0 of decoupleR, by updating to the current version of decoupleR it will work fine. First run:
devtools::install_github('saezlab/decoupleR')
Then by running this:
library(decoupleR)
minimal_matrix <- data.frame("Gene" = c("gene1", "gene2", "gene3"),
"t" = c(3, -3, 1)) %>%
tibble::column_to_rownames("Gene") %>%
as.matrix()
minimal_network <- data.frame("source" = c("TF1"),
"target" = c("gene1", "gene2"),
"mor" = c(1, -1),
"likelihood" = c(10, 10))
decoupleR::run_ulm(mat = minimal_matrix, network = minimal_network, minsize=0)
You should get this:
# A tibble: 1 × 5
statistic source condition score p_value
<chr> <chr> <chr> <dbl> <dbl>
1 mlm TF1 t 5.20 0.121
I modified the example (basically added one more gene) so that it would return a valid output. Please let me know if this solves the issue or if you run with any more problems.
Thank you Pau, I forced a reinstallation devtools::install_github('saezlab/decoupleR', force = TRUE)
, and restarted my R session and everything is working!
This error occurs for me with
run_mlm
andrun_ulm
but it doesn't affect other functions such asrun_wmean
.Minimum reproducible example:
rlang::last_trace()
gives:Session Info: