Merge pull request #41 from bahlolab/devel_speedy

v0.88.2 Small speed improvement (1.2x) of tsum_test()

Former-commit-id: ab2484a

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: exSTRa
 Type: Package
 Title: Expanded STR algorithm: detecting expansions in Illumina sequencing data
-Version: 0.88.0
-Date: 2018-08-31
+Version: 0.88.2
+Date: 2018-09-02
 Author: Rick Tankard
 Maintainer: Rick Tankard <[email protected]>
 Description: Detecting expansions with paired-end Illumina sequencing data.

R/private_functions.R

@@ -383,7 +383,7 @@ make_quantiles_matrix <- function(strscore, loc = TRUE, sample = NULL, read_coun
   }
   assert("Cannot set both probs and n.quantiles", is.null(probs) || is.null(n.quantiles))
   if(is.null(probs) && is.null(n.quantiles)) {
-    n.quantiles <- loc_data[, .N, by = sample][, quantile(N, read_count_quant, names = FALSE)] %>% round
+    n.quantiles <- round(loc_data[, .N, by = sample][, quantile(N, read_count_quant, names = FALSE)])
   }
   method <- tolower(method)
   if(method == "al1" || method == "al1_all") {
@@ -403,7 +403,7 @@ make_quantiles_matrix <- function(strscore, loc = TRUE, sample = NULL, read_coun
     stop('"Please choose type for quantile with method = "quantile#"')
   }
   if(grepl("^quantile\\d", method)) {
-    quantile_type <- sub("quantile", "", method) %>% as.numeric()
+    quantile_type <- as.numeric(sub("quantile", "", method))
     method <- "quantile"
   }
   assert("samples is not the key of strscore$samples", key(strscore$samples)[1] == "sample")
@@ -440,15 +440,15 @@ make_quantiles_matrix <- function(strscore, loc = TRUE, sample = NULL, read_coun
       }
       v <- sort(v)
     } else if(method == "al1_all") {
-      v <- munoz_rueda_al1(y, n.quantiles) %>% sort
+      v <- sort(munoz_rueda_al1(y, n.quantiles))
     } else {
       stop("Undefined method ", method)
     }
     quant.matrix[sampi, ] <- v
   }
   rownames(quant.matrix) <- sample
   # remove NA rows
-  low.count.samples <- apply(quant.matrix, 1, function(x) { is.na(x) %>% all })
+  low.count.samples <- apply(quant.matrix, 1, function(x) { all(is.na(x)) })
   quant.matrix <- quant.matrix[!low.count.samples, ]
   list(x = probs, y.mat = quant.matrix, low.count = names(low.count.samples[low.count.samples]))
 }

R/tsum_test.R

@@ -303,7 +303,7 @@ tsum_statistic_1locus <- function(
       sqm <- t (replicate(N, rnorm(M, mu_vec, se_vec)))
       # as this means the quantiles of a sample are no longer ordered, we sort
       for(i in seq_len(N)) {
-        sqm[i, ] <- sort.int(sqm[i,  ])
+        sqm[i, ] <- sort.int(sqm[i,  ], method = "shell")
       }
       sqm
     }