One can write an expression set into a csv file using csv.write. For example, using the standard bladderbatch bioconductor package the following code writes a csv file to the current working drectory:
library("bladderbatch")
data("bladderdata")
write.csv(bladderEset, "bladderEset.csv")
Is there a tool which can read the produced csv file back into R as an expressionSet?
If not, is there a eset ↔ csv serialiser/deserialiser, which can both output esets as csv files and read csv files as esets?
The reason I'm asking is because I need to interact with esets with python and java code, and I can easily work with "csv" files, but not with ".rda", ".CEL" or other binary files.
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written
by
popantrop •
1 answer
To read it back in, use read.csv("bladderEset.csv").
To convert to an eset object, use the ExpressionSet package and function, and supply your data-matrix as the assayData parameter. You can also set the phenotype data.
Further reading: https://www.rdocumentation.org/packages/Biobase/versions/2.32.0/topics/ExpressionSet
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