Skip to content

Create metacell_funcs.R #9

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

Closed
Ann-Holmes wants to merge 1 commit into from
Closed

Create metacell_funcs.R #9

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
5 changes: 3 additions & 2 deletions R/metacell_funcs.R
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,6 +26,7 @@ KNN <- function(dist.mat, k = 5){
#' @return A list of meta cell matrices for all clusters with enough samples.
#' @export
MetaCells <- function(counts.mat, dist.mat, clust.vect, num.neighbors = 5, subset = 250, min.samps = 500) {
n <- subset
counts.mat <- as.matrix(counts.mat)
dist.mat <- as.matrix(dist.mat)
# dummy clustering vector if not specified
Expand All @@ -47,12 +48,12 @@ MetaCells <- function(counts.mat, dist.mat, clust.vect, num.neighbors = 5, subse
knn.mat <- KNN(clust.dist, k = num.neighbors)
if (is.null(subset)) {
sub.samps <- clust.samps
subset <- length(sub.samps)
n <- length(sub.samps)
} else {
sub.samps <- sample(clust.samps, subset)
}
# impute matrix
imp.mat <- matrix(0L, nrow = nrow(clust.counts), ncol = subset)
imp.mat <- matrix(0L, nrow = nrow(clust.counts), ncol = n)
rownames(imp.mat) <- rownames(counts.mat); colnames(imp.mat) <- sub.samps
for (ss in sub.samps) {
neighbor.vect <- c(ss, rownames(knn.mat)[knn.mat[ss,]])
Expand Down