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markziemann / dee2

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data
http://dee2.io
GNU General Public License v3.0
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'getDEE2' function could failed to return DEE2 data if .tsv files contain '#' character #77

Closed uilnauyis closed 4 years ago

uilnauyis commented 4 years ago

For example, the sample_name of sample 'SRR6025297' is '57220_H9_hESC_CSDE1shRNA#2replicate#3'. If this sample is requested, 'getDEE2' function fails to return the data object, because 'read.table' function treats character '#' as the special character for comments and thus failed to read the 'MetadataFull.tsv' file.

I suggest to add 'comment.char = '' ' as an argument for all 'read.table' in dee2/getDEE2/R/getDEE2.R to avoid this problem. I could create a pull request for fixing this issue if you'd like to.

markziemann commented 4 years ago

Many thanks for reporting this bug. I will have a fix soon.

markziemann commented 4 years ago

Hello @uilnauyis could you try reinstalling and see if it works? Thanks

uilnauyis commented 4 years ago

Awesome! I could confirm the bug has been fixed now. Thanks!