derfinderReport {regionReport} | R Documentation |
This function generates a HTML report exploring the basic results from single base-level approach derfinder analysis results (www.bioconductor.org/packages/derfinder). The HTML report itself is generated using rmarkdown (http://rmarkdown.rstudio.com/). It works best after using mergeResults.
derfinderReport(prefix, outdir = "basicExploration", output = "basicExploration", project = prefix, browse = interactive(), nBestRegions = 100, makeBestClusters = TRUE, nBestClusters = 2, fullCov = NULL, hg19 = TRUE, p.ideos = NULL, txdb = NULL, device = "png", significantVar = "qvalue", customCode = NULL, template = NULL, theme = NULL, digits = 2, ...)
prefix |
The main data directory path where
mergeResults was run. It should be the same as
|
outdir |
The name of output directory relative to |
output |
The name of output HTML file (without the html extension). |
project |
The title of the project. |
browse |
If |
nBestRegions |
The number of region plots to make, ordered by area. |
makeBestClusters |
If |
nBestClusters |
The number of region cluster plots to make by taking
the |
fullCov |
A list where each element is the result from
loadCoverage used with |
hg19 |
If |
p.ideos |
A list where each element is the result of
plotIdeogram. If it's |
txdb |
Specify the transcription database to use for making the plots
for the top regions by area. If |
device |
The graphical device used when knitting. See more at
http://yihui.name/knitr/options ( |
significantVar |
A character variable specifying whether to use the
p-values, the FDR adjusted p-values or the FWER adjusted p-values to
determine significance. Has to be either |
customCode |
An absolute path to a child R Markdown file with code to be evaluated before the reproducibility section. Its useful for users who want to customize the report by adding conclusions derived from the data and/or further quality checks and plots. |
template |
Template file to use for the report. If not provided, will use the default file found in basicExploration/basicExploration.Rmd within the package source. |
theme |
A ggplot2 theme to use for the plots made with ggplot2. |
digits |
The number of digits to round to in the interactive table of
the top |
... |
Arguments passed to other methods and/or advanced arguments. Advanced arguments:
Passed to extendedMapSeqlevels. |
Set output_format
to 'knitrBootstrap::bootstrap_document'
or
'pdf_document'
if you want a HTML report styled by knitrBootstrap or
a PDF report respectively. If using knitrBootstrap, we recommend the version
available only via GitHub at https://github.com/jimhester/knitrBootstrap
which has nicer features than the current version available via CRAN. You can
also set the output_format
to 'html_document'
for a HTML
report styled by rmarkdown. The default is set to
'BiocStyle::html_document'
.
If you modify the YAML front matter of template
, you can use other
values for output_format
.
The HTML report styled with knitrBootstrap can be smaller in size than the
'html_document'
report.
An HTML report with a basic exploration of the derfinder results.
Leonardo Collado-Torres
mergeResults, analyzeChr, fullCoverage
## Load derfinder library('derfinder') ## The output will be saved in the 'derfinderReport-example' directory dir.create('derfinderReport-example', showWarnings = FALSE, recursive = TRUE) ## For convenience, the derfinder output has been pre-computed file.copy(system.file(file.path('extdata', 'chr21'), package='derfinder', mustWork=TRUE), 'derfinderReport-example', recursive = TRUE) ## Not run: ## If you prefer, you can generate the output from derfinder initialPath <- getwd() setwd(file.path(initialPath, 'derfinderReport-example')) ## Collapse the coverage information collapsedFull <- collapseFullCoverage(list(genomeData$coverage), verbose=TRUE) ## Calculate library size adjustments sampleDepths <- sampleDepth(collapsedFull, probs=c(0.5), nonzero=TRUE, verbose=TRUE) ## Build the models group <- genomeInfo$pop adjustvars <- data.frame(genomeInfo$gender) models <- makeModels(sampleDepths, testvars=group, adjustvars=adjustvars) ## Analyze chromosome 21 analyzeChr(chr='21', coverageInfo=genomeData, models=models, cutoffFstat=1, cutoffType='manual', seeds=20140330, groupInfo=group, mc.cores=1, writeOutput=TRUE, returnOutput=FALSE) ## Change the directory back to the original one setwd(initialPath) ## End(Not run) ## Merge the results from the different chromosomes. In this case, there's ## only one: chr21 mergeResults(chrs = '21', prefix = 'derfinderReport-example', genomicState = genomicState$fullGenome) ## Load the options used for calculating the statistics load(file.path('derfinderReport-example', 'chr21', 'optionsStats.Rdata')) ## Generate the HTML report report <- derfinderReport(prefix='derfinderReport-example', browse=FALSE, nBestRegions=1, makeBestClusters=FALSE, fullCov=list('21'=genomeDataRaw$coverage), optionsStats=optionsStats) if(interactive()) { ## Browse the report browseURL(report) } ## Not run: ## Note that you can run the example using: example('derfinderReport', 'regionReport', ask=FALSE) ## End(Not run)