Skip to content
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

fix: logical in ModelNegativeADTnorm.r #47

Merged
merged 2 commits into from
Jun 15, 2024
Merged

fix: logical in ModelNegativeADTnorm.r #47

Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
84b3cd6
fix: logical in ModelNegativeADTnorm.r
maxkarlsson May 31, 2024
73d58b1
fix: error in warning message
maxkarlsson May 31, 2024
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
11 changes: 6 additions & 5 deletions R/ModelNegativeADTnorm.r
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,17 +137,18 @@ ModelNegativeADTnorm = function(cell_protein_matrix,
mclust::Mclust(data = x, G = 2, verbose = FALSE, warn = FALSE)
})
mu1 = unlist(lapply(p.model, function(x) x$parameters$mean[[1]]))
if (isFALSE(all.equal(length(mu1), length(rownames(adt_log))))) {
if (isFALSE(length(mu1) == length(rownames(adt_log)))) {
ad_name = setdiff(rownames(adt_log), names(mu1))
warning(
paste0('empirical background cound not be fit for: ',
ad_name,
' value returned will be log transformed without background correction'),
paste0('empirical background cound not be fit for ',
length(ad_name), ' proteins: ',
paste(ad_name, collapse = ', '),
'. Value returned will be log transformed without background correction.')
)
ad = as.numeric(rep(x = 0, length(ad_name)))
names(ad) = ad_name
mu1 = c(mu1 , ad)
mu1 = mu1[match(rownames(norm_adt) , names(mu1) )]
mu1 = mu1[match(rownames(adt_log) , names(mu1) )]
}
norm_adt = apply( adt_log, 2, function(x) (x - mu1) )

Expand Down