Merge pull request #50 from AnqiWang2021/master

fix list name
stephenslab · Mar 17, 2024 · 308b496 · 308b496
2 parents f999c14 + 5287a73
commit 308b496
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Showing 2 changed files with 19 additions and 5 deletions.
diff --git a/R/mash.R b/R/mash.R
@@ -47,9 +47,22 @@ create_mixture_prior = function (mixture_prior, R, null_weight = NULL,
     if(!("matrices" %in% names(mixture_prior))){
       stop("mixture_prior must contain 'matrices'.")
     }
-    if (is.null(mixture_prior$weights))
+    if (is.null(mixture_prior$weights)) {
       mixture_prior$weights = rep(1/length(mixture_prior$matrices),
                                   length(mixture_prior$matrices))
+    }
+    if(!is.null(include_indices)) {
+       mixture_prior$matrices <- lapply(mixture_prior$matrices, function(x, to_keep) {
+                                           x[to_keep, to_keep]
+                                          }, include_indices)
+    }
+    #Check whether the elements of the each matrix are equal to zero and record the corresponding index
+    null_matrix_index <- which(sapply(mixture_prior$matrices, function(mat) all(mat == 0)))
+    #Remove the corresponding indices in matrices 
+    if (length(null_matrix_index) > 0) {
+       mixture_prior$matrices <- mixture_prior$matrices[-null_matrix_index]
+    }                                  
+    mixture_prior$weights <- mixture_prior$weights[-null_matrix_index]/sum(mixture_prior$weights[-null_matrix_index])
     return(MashInitializer$new(NULL,NULL,xUlist = mixture_prior$matrices,
                                prior_weights = mixture_prior$weights,
                                null_weight = null_weight,

diff --git a/R/mash_regression.R b/R/mash_regression.R
@@ -290,8 +290,9 @@ MashInitializer <- R6Class("MashInitializer",
         xUlist = mashr:::expand_cov(Ulist,grid,usepointmass = TRUE)
       } else {
         if (!all(xUlist[[1]] == 0))
-          xUlist = c(list(matrix(0,nrow(xUlist[[1]]),ncol(xUlist[[1]]))),
-                     xUlist)
+          xUlist = c(list(null_model = matrix(0,nrow(xUlist[[1]]),ncol(xUlist[[1]]),
+                                      dimnames = list(rownames= rownames(xUlist[[1]]), colnames = colnames(xUlist[[1]])))),
+                          xUlist)
       }
       if (!is.null(include_conditions)) {
         for (l in 1:length(xUlist)) {
@@ -349,7 +350,7 @@ MashInitializer <- R6Class("MashInitializer",
       if (length(unique(u_rows)) > 1)
         stop("Ulist contains matrices of different dimensions")
       prior_weights = prior_weights/sum(prior_weights)
-      private$xU = list(pi = c(null_weight,prior_weights * (1 - null_weight)),
+      private$xU = list(pi = c(null_model = null_weight,prior_weights * (1 - null_weight)),
                         xUlist = xUlist)
 
       return(invisible(self))
@@ -461,4 +462,4 @@ MashInitializer <- R6Class("MashInitializer",
     xU       = NULL,
     inv_mats = NULL
   )
-)
+)