How to save results of each step from ChAMP pipeline?
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Federica ▴ 10
@federica-24874
Last seen 4 months ago
Italy

Hi everyone,

I'm trying to test a pipeline to analyse methylation array data using ChAMP package.

I'm following the follow tutorial:

https://www.bioconductor.org/packages/release/bioc/vignettes/ChAMP/inst/doc/ChAMP.html

Now, I'm wondering: how can I save the results of each step of ChAMP pipeline? It seems to me that it'd be necessary to do it manually using a command in R.

For example, I've performed the filtering step by running the following commands:

myImport <- champ.import(testDir)
myLoad <- champ.filter()

The results of the previous commands are simply reported on the shell of R and they aren't saved in any format in my working directory. How can I save these results? And which format should I use to save them?

Thank u!

Bioconductor ChAMP • 126 views
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Yuan Tian ▴ 240
@yuan-tian-13904
Last seen 15 days ago
United Kingdom

Hi Federica:

Each step in ChAMP pipeline should generate a R object, which could be list, dataframe, vector. etc. You can save it like a normal R objects like save(myLoad, file="myLoad.RData"), then you can reload them anytime you want.

However, it's not easy to save them into a "easy to open" format like Excel, txt, because as I said there are lists, dataframe, vectors in it. Personally I suggest people firstly check what are these returned result via R, like using head() function, and read manual. Then for some key results, for example dataframe result from champ.DMP(), you may save it into Excel like: write_xls(myDMP[[1]], "DMPExcelTable.xlsx")

Best Tian

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