Dump all of curatedMetagenomicData as two .csv files

Source: R/dataDump.R

Dump all of curatedMetagenomicData as two .csv files

dataDump(dataType = "relative_abundance", counts = FALSE)

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) {
   tse <- dataDump()
   tse
   dir(pattern = "\\.csv")
}