lcolladotor

hola
===


asfd

```{r}
print('hola')
x <- 1
x

lcolladotor

## Fix as best as possible the bug in calculatePvalues() regarding the default
## maxRegionGap value.

## Usage:
# Step 1: open R in the main results folder
# Step 2: use fixChrs() with options of your choice
# fixChrs('chr')

## Alternatively use fixRegions() manually and re-run 
## bumphunter::annotateNearest()

lcolladotor

## Visualizing the error
## Modified from https://github.com/lcolladotor/derfinderPlot/blob/master/tests/testthat/test_adv-plotCluster.R

library('derfinder')

## Collapse the coverage information
collapsedFull <- collapseFullCoverage(list(genomeDataRaw), verbose=TRUE)

## Calculate library size adjustments
sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5), nonzero=TRUE, 

lcolladotor

> ## Visualizing the error
> ## Modified from https://github.com/lcolladotor/derfinderPlot/blob/master/tests/testthat/test_adv-plotCluster.R
> 
> library('derfinder')
> 
> ## Collapse the coverage information
> collapsedFull <- collapseFullCoverage(list(genomeDataRaw), verbose=TRUE)
2014-11-22 17:38:06 collapseFullCoverage: Sorting fullCov
2014-11-22 17:38:06 collapseFullCoverage: Collapsing chromosomes information by sample
> 

lcolladotor

---
title: "test"
output: pdf_document
---

This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see <http://rmarkdown.rstudio.com>.

When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:

```{r}

lcolladotor

$ R

R version 3.1.1 Patched (2014-10-16 r66782) -- "Sock it to Me"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

lcolladotor

> library('GenomicRanges')
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,

lcolladotor

library('derfinder')
library('BiocParallel')

## Check that the cluster is correctly defined
## Aka, that it's a MulticoreParam class instead of the default SnowParam
x <- derfinder:::.define_cluster(BPPARAM.custom = MulticoreParam(workers = 2))
x

## Collapse the coverage information
collapsedFull <- collapseFullCoverage(list(genomeData$coverage),

lcolladotor

library('BiocParallel')

## Run bplapply example code with MulticoreParam
system.time(result <- bplapply(1:10, function(v) {
    message("working") ## 10 tasks
    sqrt(v)
}, BPPARAM = MulticoreParam(workers = 2)))
result[[1]]

## Run bplapply example code with SnowParam

lcolladotor

> x <- parallel::mclapply(1:10, sqrt)
> cl <- parallel::makeCluster(10, "PSOCK")
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout
Loading required package: colorout