Remove un-used codes and use && instead of & in condition.

DavisLaboratory · Mar 26, 2024 · 892a8f3 · 892a8f3
1 parent 34bf266
commit 892a8f3
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Showing 2 changed files with 4 additions and 6 deletions.
diff --git a/R/tf_idf_iae_wrappers.R b/R/tf_idf_iae_wrappers.R
@@ -79,7 +79,6 @@ idf <- function(expr, features = NULL, thres = 0) {
 #' smartid:::idf_m(data)
 idf_m <- function(expr, features = NULL, thres = 0) {
   if (is.null(features)) features <- seq_len(nrow(expr))
-  n_obs <- ncol(expr) ## number of total obs
 
   # thres <- 0
   # thres <- sparseMatrixStats::rowQuantiles(expr, probs = 0.25, na.rm = TRUE)
@@ -359,7 +358,6 @@ iae <- function(expr, features = NULL, thres = 0) {
 #' smartid:::iae_m(data)
 iae_m <- function(expr, features = NULL, thres = 0) {
   if (is.null(features)) features <- seq_len(nrow(expr))
-  n_obs <- ncol(expr) ## number of total obs
 
   # thres <- 0
   # thres <- sparseMatrixStats::rowQuantiles(expr, probs = 0.25, na.rm = TRUE)

diff --git a/R/top_markers.R b/R/top_markers.R
@@ -65,9 +65,9 @@ top_markers_abs <- function(data, label, n = 10,
                             scale = TRUE, use.mgm = TRUE,
                             softmax = TRUE) {
   method <- match.arg(method)
-  if (scale & use.mgm) {
+  if (scale && use.mgm) {
     data <- scale_mgm(expr = data, label = label)
-  } else if (scale & !use.mgm) {
+  } else if (scale && !use.mgm) {
     ## scale scores on rows
     # mu_s <- sparseMatrixStats::rowMeans2(data, na.rm = TRUE)
     # sd_s <- sparseMatrixStats::rowSds(data, na.rm = TRUE)
@@ -126,15 +126,15 @@ top_markers_glm <- function(data, label, n = 10,
   label <- factor(label) # factorize label
 
   ## scale
-  if (scale & !use.mgm) {
+  if (scale && !use.mgm) {
     ## scale scores on rows
     # mu_s <- sparseMatrixStats::rowMeans2(data, na.rm = TRUE)
     # sd_s <- sparseMatrixStats::rowSds(data, na.rm = TRUE)
     # data <- (data - mu_s) / sd_s
 
     data <- t(scale(t(data)))
     data[is.na(data)] <- 0 # assign 0 to NA when sd = 0
-  } else if (scale & use.mgm) {
+  } else if (scale && use.mgm) {
     data <- scale_mgm(expr = data, label = label)
   }