correlate_covariates: redundant conversion to numeric and incorrect warning
#152
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While trying to create a more reproducible example with example data. I followed the checks from line 32. library(ggplot2)
library(MOFA2)
# Create example data
data <- make_example_data(
n_views = 2,
n_samples = 200,
n_features = 100,
n_factors = 10
)[[1]]
# Add metadata
N <- ncol(data[[1]])
groups <- c(rep("A", N / 2), rep("B", N / 2))
# Create MOFA object
MOFAobject <- create_mofa(data, groups = groups)
# Prepare MOFA object
MOFAobject <- prepare_mofa(
object = MOFAobject
)
# Train MOFA
outfile <- file.path(tempdir(), "model.hdf5")
MOFAobject.trained <- run_mofa(MOFAobject, outfile, use_basilisk = TRUE)
# For better readability
model <- MOFAobject.trained
# Assign some metadata to covariates table
nums <- runif(200, 0, 1000)
covariates <- data.frame(nums = nums)
metadata <- samples_metadata(model)
samples <- metadata$sample
rownames(covariates) <- samples_metadata(model)$sample
# Run function
correlate_factors_with_covariates(
object = model,
covariates = covars
)Error in correlate_factors_with_covariates(object = model, covariates = covars) :
all(rownames(covariates) %in% samples) is not TRUEBut they are if I follow the checks: all(rownames(covariates) %in% samples)[1] TRUENot sure about this, but I can open an issue. |
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In
correlate_covariates.Ron line 52 the code converts the columns to numeric twice with a warning in between. Line 56 is not required. We can throw a warning and then convert the columns to numeric.Another issue is that if I run this function on with a covariate
data.framewhich is numeric, I still get this warning.Below, I generate some numbers and assign them to a column
I confirm that
covarsdata.frame doesn't only contains numeric values:If I run the code from the function, I don't get this warning
maeis my MultiAssayExperiment object.The text was updated successfully, but these errors were encountered: