Adding Phenodata after processing in Lumi
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@marino-rebecca-bosko-4774
Last seen 8.1 years ago
Hi List, Does anyone know if it is possible to add phenoData into lumi after you process your samples rather than during import with lumiR.batch? We have close to 500 samples in 4 batches of 96 and I'm currently finding myself wanting to add or update phenoData after the import. As importing such large scale batches are taxing on my processor, it would be much easier to import the data/phenoData and be able to update the phenoData later rather than having to re-import when I decide to add another variable to the phenoData. I'm relatively new to R, bioconductor, and lumi so I don't know if there is a well known method to do this that I'm currently unfamiliar with. Any help would be much appreciated. Thanks for any Advice, Becky Marino [[alternative HTML version deleted]]
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Chi Hong • 0
@chi-hong-7095
Last seen 6.7 years ago
United States

See if this helps:

Adding a column to phenoData dataframe

 

In addition, if you have a separate phenotype file that you'd like to add, you do something like:

pData(lumiBatch.object) = phenotype.file

or

pData(lumiBatch.object) = merge( x=pData(lumiBatch.object), y=phenotype.file, by.x="sampleID", by.x="ID.in.phenotype.file", all=TRUE)

 

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