Dump all of curatedMetagenomicData as two .csv files
Arguments
- dataType
(default: "relative_abundance") Data type, passed on to
returnSamples
.- counts
(Default: FALSE) Whether to convert to count-like data by multiplying through by read depth. Passed on to
returnSamples
.
Value
The SummarizedExperiment or TreeSummarizedExperiment containing all of cMD for the data type requested. Calling this function has the side-effect of also writing two csv files, one for the assay data of this object and one for the colData.
Details
This function also removes control samples from the NielsenHB_2014 study, which are duplicated in the LeChatelierE_2013 study. The cMD version number is put in the filename.
Examples
if (FALSE) { # \dontrun{
tse <- dataDump()
tse
dir(pattern = "\\.csv")
} # }