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bhklab / MetaGxBreast

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could not find download options for TCGA and metabric. #2

Closed wangt-biotime closed 4 years ago

wangt-biotime commented 5 years ago

How can we get TCGA and METABRIC datasets using MetaGxBreast?

mzon7 commented 4 years ago

The datasets can be loaded together by using, breastEsets = loadBreastEsets(loadString = c("METABRIC", "TCGA")). Unfortunately the strings are case sensitive, I will try to remove this in a future update. I would recommend using allBreastData = loadBreastDatasets(). Esets are officially outdated objects and have been replaced by the summarizedExperiments object class. The loadBreastDatasets() function has the exact same expression data as the loadBreastEsets() function but instead loads the data as summarizedExperiments . Plus the simple command loadBreastDatasets() will obtain all of the data sets and then you can choose which ones to use once you have them all in your work space.