rnb.run.analysis {RnBeads} | R Documentation |
Starts the RnBeads analysis pipeline on the given dataset. It loads the dataset if it is specified as a location.
rnb.run.analysis( dir.reports, data.source = NULL, sample.sheet = NULL, data.dir = NULL, GS.report = NULL, GEO.acc = NULL, data.type = rnb.getOption("import.default.data.type"), initialize.reports = TRUE, build.index = TRUE, save.rdata = TRUE )
dir.reports |
Directory to host the generated report files. This must be a |
data.source |
Methylation dataset as an object of type inheriting |
sample.sheet |
A spreadsheet-like text file with sample annotations. The required columns are different
for different values of |
data.dir |
For |
GS.report |
GenomeStudio report file. |
GEO.acc |
Gene Expression Omnibus accession of the data series with HumanMethylation450 data.
|
data.type |
|
initialize.reports |
Flag indicating if the report's directory must be initialized. If this parameter is set to
|
build.index |
Flag indicating if a report index file (named |
save.rdata |
Flag indicating whether important data objects (the filtered and unfiltered RnBSets, differential methylation) should be saved to an RData file in the reports folder. |
Invisibly, the loaded, normalized and/or possibly filtered dataset as an object of type inheriting
RnBSet
.
Yassen Assenov