When using all_zc() function as detailed in the vignette:
"Error in eval(substitute(expr), envir, enclos) :
object 'pvalue' not found"
This part of the vignette:
zc_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/zero_coverage.txt")) zc_samples <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", zc_fnames) %>% sub("zero_coverage.txt", "", .) %>% gsub("/", "", .) zc_conditions <- sub("[0-9]+", "", zc_samples) all_zc <- get_batch_intron_zc(zc_fnames, zc_samples, zc_conditions) head(all_zc)
This was fixed for me by setting the .keep_all parameter of the distinct() dplyr function to TRUE distinct(.keep_all = TRUE) within the zero_coverage.R file.
When using all_zc() function as detailed in the vignette:
"Error in eval(substitute(expr), envir, enclos) : object 'pvalue' not found"
This part of the vignette:
zc_fnames <- Sys.glob(file.path(base_dir, "experiment/*/*/zero_coverage.txt")) zc_samples <- sub(file.path(base_dir, "experiment/[a-z]+/"), "", zc_fnames) %>% sub("zero_coverage.txt", "", .) %>% gsub("/", "", .) zc_conditions <- sub("[0-9]+", "", zc_samples) all_zc <- get_batch_intron_zc(zc_fnames, zc_samples, zc_conditions) head(all_zc)This was fixed for me by setting the .keep_all parameter of the distinct() dplyr function to TRUE
distinct(.keep_all = TRUE)within the zero_coverage.R file.Rupert