automation

R/functions.R

@@ -905,7 +905,7 @@ test.multiple <- function(Y,X,map,rho=c(0,0.5,1),spec=1){
     if(TRUE){
         max <- p/0.05+1
         limit <- ceiling(0.05*max/p)
-        steps <- diff(limit^seq(from=1,to=log(max)/log(limit),length.out=pmin(p,50))) # was (p,20)
+        steps <- diff(limit^seq(from=1,to=log(max)/log(limit),length.out=pmin(p,20))) # was (p,20)
         steps <- c(limit,round(steps)) # Or replace "limit" by "minimum # of permutations"!
         steps[length(steps)] <- max-sum(steps[-length(steps)])
     }

docs/articles/vignette.html

@@ -193,10 +193,10 @@
 <a class="sourceLine" id="cb5-8" data-line-number="8">        <span class="co">#    if(wait){Sys.sleep(60);cat(".")}</span></a>
 <a class="sourceLine" id="cb5-9" data-line-number="9">        <span class="co">#}  </span></a>
 <a class="sourceLine" id="cb5-10" data-line-number="10">        </a>
-<a class="sourceLine" id="cb5-11" data-line-number="11">        <span class="kw">rm</span>(<span class="dt">list=</span><span class="kw">setdiff</span>(<span class="kw">ls</span>(),<span class="kw">c</span>(<span class="st">"data"</span>,<span class="st">"chr"</span>,<span class="st">"path"</span>))); <span class="kw">gc</span>()</a>
-<a class="sourceLine" id="cb5-12" data-line-number="12">        <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"temp."</span>,data,<span class="st">".chr"</span>,chr,<span class="st">".RData"</span>)))</a>
-<a class="sourceLine" id="cb5-13" data-line-number="13">        pvalue &lt;-<span class="st"> </span>spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/test.multiple">test.multiple</a></span>(<span class="dt">Y=</span>exons,<span class="dt">X=</span>snps,<span class="dt">map=</span>map,<span class="dt">rho=</span><span class="dv">1</span>,<span class="dt">spec=</span><span class="dv">20</span>)</a>
-<a class="sourceLine" id="cb5-14" data-line-number="14">        <span class="kw">save</span>(<span class="dt">object=</span>pvalue,<span class="dt">file=</span><span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval."</span>,data,<span class="st">".chr"</span>,chr,<span class="st">".RData"</span>)))</a>
+<a class="sourceLine" id="cb5-11" data-line-number="11">        <span class="kw">rm</span>(<span class="dt">list=</span><span class="kw">setdiff</span>(<span class="kw">ls</span>(),<span class="kw">c</span>(<span class="st">"data"</span>,<span class="st">"chr"</span>,<span class="st">"path"</span>))); <span class="kw">gc</span>(); <span class="kw">cat</span>(<span class="st">"."</span>)</a>
+<a class="sourceLine" id="cb5-12" data-line-number="12">        <span class="kw">load</span>(<span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"temp."</span>,data,<span class="st">".chr"</span>,chr,<span class="st">".RData"</span>))); <span class="kw">cat</span>(<span class="st">"."</span>)</a>
+<a class="sourceLine" id="cb5-13" data-line-number="13">        pvalue &lt;-<span class="st"> </span>spliceQTL<span class="op">::</span><span class="kw"><a href="http://www.rdocumentation.org/packages/spliceQTL/topics/test.multiple">test.multiple</a></span>(<span class="dt">Y=</span>exons,<span class="dt">X=</span>snps,<span class="dt">map=</span>map,<span class="dt">rho=</span><span class="dv">1</span>,<span class="dt">spec=</span><span class="dv">1</span>); <span class="kw">cat</span>(<span class="st">"."</span>)</a>
+<a class="sourceLine" id="cb5-14" data-line-number="14">        <span class="kw">save</span>(<span class="dt">object=</span>pvalue,<span class="dt">file=</span><span class="kw">file.path</span>(path,<span class="kw">paste0</span>(<span class="st">"pval."</span>,data,<span class="st">".chr"</span>,chr,<span class="st">".RData"</span>))); <span class="kw">cat</span>(<span class="st">"</span><span class="ch">\n</span><span class="st">"</span>)</a>
 <a class="sourceLine" id="cb5-15" data-line-number="15">    }</a>
 <a class="sourceLine" id="cb5-16" data-line-number="16"><span class="co">#q()</span></a>
 <a class="sourceLine" id="cb5-17" data-line-number="17"><span class="co">#n</span></a>

vignettes/vignette.Rmd

@@ -116,7 +116,7 @@ for(chr in 1:22){
 }
 ```
 
-On the virtual machine, first restart R and then execute this chunk to test for alternative splicing. (It seems that lme4::lmer in spliceQTL::adjust.covariates fails to release  memory on Linux.)
+On the virtual machine, first restart R and then execute this chunk to test for alternative splicing. (It seems that lme4::lmer in spliceQTL::adjust.covariates fails to release memory on Linux.)
 
 ```{r test,eval=FALSE}
 for(chr in 22:1){
@@ -129,10 +129,10 @@ for(chr in 22:1){
         #    if(wait){Sys.sleep(60);cat(".")}
         #}  
         
-        rm(list=setdiff(ls(),c("data","chr","path"))); gc()
-        load(file.path(path,paste0("temp.",data,".chr",chr,".RData")))
-        pvalue <- spliceQTL::test.multiple(Y=exons,X=snps,map=map,rho=1,spec=20)
-        save(object=pvalue,file=file.path(path,paste0("pval.",data,".chr",chr,".RData")))
+        rm(list=setdiff(ls(),c("data","chr","path"))); gc(); cat(".")
+        load(file.path(path,paste0("temp.",data,".chr",chr,".RData"))); cat(".")
+        pvalue <- spliceQTL::test.multiple(Y=exons,X=snps,map=map,rho=1,spec=1); cat(".")
+        save(object=pvalue,file=file.path(path,paste0("pval.",data,".chr",chr,".RData"))); cat("\n")
     }
 #q()
 #n