Calculate difference - label shuffling error

[dBenedek]

I encountered the following error when running calculate_difference() with label shuffling:
Error in ecdf(shuffled[i, ]) : 'x' must have 1 or more non-missing values

It turned out that some rows (genes) with only 0 values caused the issue.
Would be nice to find a solution/recommendation on how to handle this problem (e.g. by simply dropping genes with only 0s before difference calculation or something else).

Another issue related to this problem: after calculating diversity, there are some rows with a few really low values (values < .Machine$double.eps), that are handled as 0s so these rows also cause errors:

Error in if (ecdf(shuffled[i, ])(log2_fc[i]) >= 0.5) { : 
  missing value where TRUE/FALSE needed
Calls: calculate_difference -> label_shuffling
In addition: There were 50 or more warnings (use warnings() to see the first 50)

I avoided this issue with some pre-filtering:

# Convert really small values to 0s:
diversity_data[.Machine$double.eps > diversity_data] <- 0

# Filter out samples with only zeros:
diversity_data_filtered <- diversity_data %>% 
  mutate(rowsum=rowSums(select(., starts_with("dataset")))) %>% 
  filter(rowsum != 0) %>% 
  dplyr::select(-rowsum)

[dBenedek]

I also get the error message for a row with 2 unique values and some additional 0s and NAs:

> diversity_data_filtered[404,]

                    ID dataset3_SRX4143134 dataset3_SRX4143118 dataset3_SRX4143107 dataset3_SRX4143157
404 ENSG00000030304.14                  NA          0.03355015                  NA                  NA
    dataset3_SRX4143185 dataset3_SRX4143142 dataset3_SRX4143119 dataset3_SRX4143193 dataset3_SRX4143122
404                   0                   0                   0                  NA            0.999901
    dataset3_SRX4143121
404                   0

difference <- calculate_difference(diversity_data_filtered[404:405,], # 404 - problematic row
                                   samples_data,
                                   control = "control",
                                   method = "mean",
                                   test = "shuffle")

# --> Error in if (ecdf(shuffled[i, ])(log2_fc[i]) >= 0.5) { : 
#  missing value where TRUE/FALSE needed

I guess the reason for this is that the sample number (columns) is low (10), and there are only 2 non-zero/non-NA values, so there will be some problematic groups during the shuffling procedure.