automation

R/functions.R

@@ -846,6 +846,10 @@ test.single <- function(Y,X,map,i,limit=NULL,steps=NULL,rho=c(0,0.5,1)){
 #' number of cores\strong{:}
 #' positive integer
 #' 
+#' @param min
+#' minim chunk size\strong{:}
+#' positive integer
+#' 
 #' @param steps
 #' number of iteration chunks\strong{:}
 #' positive integer
@@ -857,7 +861,7 @@ 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),spec=1,steps=20){
+test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=1,min=100,steps=20){
     
     p <- nrow(map$genes)
     
@@ -884,8 +888,8 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=1,steps=20){
     if(TRUE){
         max <- p/0.05+1
         limit <- ceiling(0.05*max/p)
-        steps <- diff(limit^seq(from=log(100),to=log(max)/log(limit),length.out=pmin(p,steps)))
-        steps[steps<100] <- 100
+        steps <- diff(limit^seq(from=log(min),to=log(max)/log(limit),length.out=pmin(p,steps)))
+        steps[steps<min] <- min
         for(i in 1:10){
             cond <- steps>10^i & steps<10^(i+1)
             steps[cond] <- ceiling(steps[cond]/10^i)*10^i 

docs/reference/test.multiple.html

@@ -120,7 +120,8 @@
     
     </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>), <span class='kw'>spec</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>steps</span> <span class='kw'>=</span> <span class='fl'>20</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'>1</span>, <span class='kw'>min</span> <span class='kw'>=</span> <span class='fl'>100</span>,
+  <span class='kw'>steps</span> <span class='kw'>=</span> <span class='fl'>20</span>)</pre>
     
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -148,6 +149,11 @@ numeric vector with values between \(0\) and \(1\)</p></td>
     <tr>
       <th>spec</th>
       <td><p>number of cores<strong>:</strong>
+positive integer</p></td>
+    </tr>
+    <tr>
+      <th>min</th>
+      <td><p>minim chunk size<strong>:</strong>
 positive integer</p></td>
     </tr>
     <tr>

man/test.multiple.Rd

@@ -4,7 +4,8 @@
 \alias{test.multiple}
 \title{Conduct multiple tests}
 \usage{
-test.multiple(Y, X, map, rho = c(0, 0.5, 1), spec = 1, steps = 20)
+test.multiple(Y, X, map, rho = c(0, 0.5, 1), spec = 1, min = 100,
+  steps = 20)
 }
 \arguments{
 \item{Y}{exon expression\strong{:}
@@ -22,6 +23,9 @@ numeric vector with values between \eqn{0} and \eqn{1}}
 \item{spec}{number of cores\strong{:}
 positive integer}
 
+\item{min}{minim chunk size\strong{:}
+positive integer}
+
 \item{steps}{number of iteration chunks\strong{:}
 positive integer}
 }