rnb.run.import {RnBeads} | R Documentation |
Functions that start the predefined modules in the RnBeads analysis pipeline.
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 )
data.source |
|
data.type |
|
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
|
show.report |
Flag indicating if the report is to be displayed after it is created. If this is,
|
rnb.set |
Methylation dataset as an object of type inheriting |
The functions start the import, quality control, preprocessing, covariate inference, tracks and tables, exploratory analysis and differential methylation modules, respectively.
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.
Yassen Assenov
rnb.run.analysis
which executes these modules in the order given above
### 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)