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lijingya / ELMER

Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
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getTCGA Error because of invalid 'description' argument #11

Open nturaga opened 9 years ago

nturaga commented 9 years ago 
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-07-0227-20A-01D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56K-01A-32D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56L-01A-31D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56N-01A-12D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/MANIFEST.txt
Error in file(file, "rt") : invalid 'description' argument

The Error happened in both BLCA and READ. The MANIFEST file itself has missing DESCRIPTION tag

f8c19c7c93155778edc6bd169d808068  README_DCC.txt
a62a715e87ca3d21027aaa10567bf042  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-07-0227-20A-01D-A39G-05.txt
0ac1003dfbab4a48bcc292630d8e314d  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56K-01A-32D-A39G-05.txt
8addef41b4dc83c315d2812027d95769  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56L-01A-31D-A39G-05.txt
7c86b5a7306b634aa8c50a9df5be98ee  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56N-01A-12D-A39G-05.txt
tiagochst commented 8 years ago

@nitesh1989 I don't know if the bug was solved, but you can use TCGAbiolinks(https://www.bioconductor.org/packages/devel/bioc/html/TCGAbiolinks.html) to download TCGA data and integrate with ELMER.