issue in input_testing

[dnarna909]

1. input_testing <- function (input, p_val_threshold = 0.05)
2. {
3. if (!is.data.frame(input)) { stop("the input is not a data frame") }
4. if (ncol(input) != 2 & ncol(input) != 3) { stop("the input should have 2 or 3 columns") }
5. if (nrow(input) < 2) { stop("There must be at least 2 rows (genes) in the input data frame") }
6. if (!is.numeric(p_val_threshold)) {stop("p_val_threshold must be a numeric value between 0 and 1") }
7. if (p_val_threshold > 1 | p_val_threshold < 0) { stop("p_val_threshold must be between 0 and 1") }
8. p_column <- ifelse(ncol(input) == 3, 3, 2)
9. if (any(is.na(input[, p_column]))) { stop("p values cannot contain NA values") }
11. if (!all(is.numeric(input[, p_column]))) { stop("p values must all be numeric") }
12. if (!all(is.numeric(input[[p_column]]))) { stop("p values must all be numeric") }
14. if (any(input[, p_column] > 1 | input[, p_column] < 0)) { stop("p values must all be between 0 and 1") }
15. message("The input looks OK")
16. }

Line 11 should be updated as Line 12 for input_testing function in this package. Otherwise error message.

[egeulgen]

I'm assuming you are using a tibble as input, hence the issue. Please use input <- as.data.frame(input) before running pathfindR as this is not the only line that may cause an issue. Meanwhile, I may try to fix all tibble-related issues and keep you updated here