automation

R/functions.R

@@ -837,6 +837,10 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
 #' correlation\strong{:}
 #' numeric vector with values between \eqn{0} and \eqn{1}
 #' 
+#' @param spec
+#' number of cores\strong{:}
+#' positive integer
+#' 
 #' @details
 #' Automatic adjustment of the number of permutations
 #' such that Bonferroni-significant p-values are possible.
@@ -844,7 +848,7 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
 #' @examples
 #' NA
 #' 
-test.multiple <- function(Y,X,map,rho=c(0,0.5,1)){
+test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=4){
     
     p <- nrow(map$genes)
     
@@ -871,7 +875,7 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1)){
     
     # parallel computation
     type <- ifelse(test=.Platform$OS.type=="windows",yes="PSOCK",no="FORK")
-    cluster <- parallel::makeCluster(spec=8,type=type)
+    cluster <- parallel::makeCluster(spec=spec,type=type)
     parallel::clusterSetRNGStream(cl=cluster,iseed=1)
     parallel::clusterExport(cl=cluster,varlist=c("Y","X","map","limit","steps","rho"),envir=environment())
     start <- Sys.time()

docs/reference/test.multiple.html

@@ -120,7 +120,7 @@
     
     </div>
 
-    <pre class="usage"><span class='fu'>test.multiple</span>(<span class='no'>Y</span>, <span class='no'>X</span>, <span class='no'>map</span>, <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fl'>1</span>))</pre>
+    <pre class="usage"><span class='fu'>test.multiple</span>(<span class='no'>Y</span>, <span class='no'>X</span>, <span class='no'>map</span>, <span class='kw'>rho</span> <span class='kw'>=</span> <span class='fu'>c</span>(<span class='fl'>0</span>, <span class='fl'>0.5</span>, <span class='fl'>1</span>), <span class='kw'>spec</span> <span class='kw'>=</span> <span class='fl'>4</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -144,6 +144,11 @@ matrix with \(n\) rows (samples) and \(q\) columns (SNPs)</p></td>
       <th>rho</th>
       <td><p>correlation<strong>:</strong>
 numeric vector with values between \(0\) and \(1\)</p></td>
+    </tr>
+    <tr>
+      <th>spec</th>
+      <td><p>number of cores<strong>:</strong>
+positive integer</p></td>
     </tr>
     </table>
     

man/test.multiple.Rd

@@ -4,7 +4,7 @@
 \alias{test.multiple}
 \title{Conduct multiple tests}
 \usage{
-test.multiple(Y, X, map, rho = c(0, 0.5, 1))
+test.multiple(Y, X, map, rho = c(0, 0.5, 1), spec = 4)
 }
 \arguments{
 \item{Y}{exon expression\strong{:}
@@ -18,6 +18,9 @@ matrix with \eqn{n} rows (samples) and \eqn{q} columns (SNPs)}
 
 \item{rho}{correlation\strong{:}
 numeric vector with values between \eqn{0} and \eqn{1}}
+
+\item{spec}{number of cores\strong{:}
+positive integer}
 }
 \description{
 This function ...