rnb.run.import: RnBeads Modules in the Analysis Pipeline

Description

Functions that start the predefined modules in the RnBeads analysis pipeline.

Usage

rnb.run.import(data.source, data.type = rnb.getOption("import.default.data.type"), dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.qc(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.preprocessing(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.inference(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.tnt(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.exploratory(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)
rnb.run.differential(rnb.set, dir.reports, init.configuration = !file.exists(file.path(dir.reports, "configuration")), close.report = TRUE, show.report = FALSE)

Arguments

data.source

character vector specifying the location of the data items on disk. The expected length of the vector differs for different values of data.type; see rnb.execute.import for a more detailed description.

data.type

character vector of length one specifying the type of the input data. The value of this parameter must be one of "idat.dir", "data.dir", "data.files", "GS.report", "GEO" or "rnb.set". See rnb.execute.import for a more detailed description.

dir.reports

Directory to host the generated report file. Note that if this directory contains files, they may be overwritten.

init.configuration

Flag indicating if the configuration directory (usually shared among reports) should also be created.

close.report

Flag indicating if the created report is to be closed using the off method.

show.report

Flag indicating if the report is to be displayed after it is created. If this is, TRUE rnb.show.report is called to open the generated HTML file.

rnb.set

Methylation dataset as an object of type inheriting RnBSet.

Value

For rnb.run.import, rnb.run.preprocessing and rnb.run.inference, the returned value is a list of two elements - the initialized or modified dataset and the created report. All other functions return the created report, invisibly.

Details

The functions start the import, quality control, preprocessing, covariate inference, tracks and tables, exploratory analysis and differential methylation modules, respectively.

Examples

Run this code


### Running the modules step by step

# Directory where your data is located
data.dir <- "~/RnBeads/data/Ziller2011_PLoSGen_450K"
idat.dir <- file.path(data.dir, "idat")
sample.annotation <- file.path(data.dir, "sample_annotation.csv")

# Directory where the output should be written to
analysis.dir <- "~/RnBeads/analysis"
# Directory where the report files should be written to
report.dir <- file.path(analysis.dir, "reports_details")
rnb.initialize.reports(report.dir)
# Set some analysis options
rnb.options(filtering.sex.chromosomes.removal = TRUE, identifiers.column = "Sample_ID")
## Restrict logging to the console only
logger.start(fname = NA)

## Data import
data.source <- c(idat.dir, sample.annotation)
result <- rnb.run.import(data.source = data.source, data.type = "idat.dir", dir.reports = report.dir)
rnb.set <- result$rnb.set

## Quality Control
rnb.run.qc(rnb.set, report.dir)

## Preprocessing
rnb.set <- rnb.run.preprocessing(rnb.set, dir.reports=report.dir)$rnb.set

## Data export
rnb.options(export.to.csv = TRUE)
rnb.run.tnt(rnb.set, report.dir)

## Exploratory analysis
rnb.run.exploratory(rnb.set, report.dir)

## Differential methylation
rnb.run.differential(rnb.set, report.dir)