Usage
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)
Arguments
dir.reports
Directory to host the generated report files. This must be a character of length one
that specifies either a non-existent path (when initialize.reports is TRUE),
or an existing directory (when initialize.reports is FALSE). In the latter
case, a call to rnb.initialize.reports might be required before viewing the
reports. data.source
Methylation dataset as an object of type inheriting RnBSet, or a
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. If set, the parameters
sample.sheet, data.dir, GS.report, GEO.acc will be ignored. sample.sheet
A spreadsheet-like text file with sample annotations. The required columns are different
for different values of data.type.
data.dir
For data.type %in% c("data.dir", "idat.dir", "bed.dir") a character singleton
specifying the location of the directory with data files. The directory should have zero
depth, i.e. should contain no subdirectories.
GS.report
GenomeStudio report file. data.type will be automatically set to "GS.report".
GEO.acc
Gene Expression Omnibus accession of the data series with HumanMethylation450 data.
data.type will be automatically set to "GEO".
data.type
character vector of length one specifying the type of the input data.
The value must be one of "data.dir", "idat.dir", "GS.report",
"GEO" or "rnb.set". See rnb.execute.import for a more detailed
description.initialize.reports
Flag indicating if the report's directory must be initialized. If this parameter is set to
TRUE, this function attempts to create the path specified by dir.reports.
Otherwise, dir.reports is expected to signify an existing directory.
build.index
Flag indicating if a report index file (named "index.html") should be created after
all modules in the pipeline complete their analyses. If this is TRUE, the index file
is also displayed using the function rnb.show.report. 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.