Skip to content

row indices of NA observations in error message #94

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
idot wants to merge 1 commit into
base: master
Choose a base branch
from
Open

row indices of NA observations in error message #94

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
7 changes: 5 additions & 2 deletions R/sample_filtering.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -56,10 +56,13 @@ simple_FNR_params = function(expr, pos_controls, fn_tresh = 0.01) {
# Median log-expression in positive observations
mu_obs = log(rowMedians(pos_expr, na.rm = TRUE))
if (any(is.na(mu_obs))) {
na_rows <- (1:nrow(expr))[pos_controls][which(is.na(mu_obs))]
na_rowsm <- paste(na_rows, sep=", ")
stop(
paste0(
"Median log-expression in positive ",
"observations NA for some positive control gene/s"
"observations NA for some positive control gene/s in rows: ",
na_rowsm
)
)
}
Expand Down Expand Up @@ -869,4 +872,4 @@ factor_sample_filter = function(expr,
warning("No z-cutoff specified, thus no filtering results returned.")
return(NA)
}
}
}