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sartorlab / methylSig

R package for DNA methylation analysis
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Methylation differences output in scientific notation #3

Closed rcavalcante closed 9 years ago

rcavalcante commented 9 years ago

Writing a methylSigDiff object to a file can result in scientific notation for methylation differences when the differences are very small. For example,

chr14 38340169 38340169 -2.37233043431928e-05 chr14 50108792 50108792 -3.51720594760074e-05 chr15 99978267 99978267 9.84861037167661e-07

gives the following error when turning a bedGraph into a bigWig (using bedGraphToBigWig):

invalid unsigned integer: "1.35e+08"

Perhaps any difference below 0.01 (or some other threshold) should be set to 0?

sartorma commented 9 years ago

Yes, adding a minimum limit like 0.01 is fine. I can’t imagine anyone being interested in a difference so small.

From: Raymond Cavalcante [mailto:notifications@github.com] Sent: Thursday, May 28, 2015 1:01 PM To: sartorlab/methylSig Subject: [methylSig] Scientific notation output of methylation differences (#3)

Writing a methylSigDiff object to a file can result in scientific notation for methylation differences when the differences are very small. For example,

chr14 38340169 38340169 -2.37233043431928e-05 chr14 50108792 50108792 -3.51720594760074e-05 chr15 99978267 99978267 9.84861037167661e-07

gives the following error when turning a bedGraph into a bigWig (using bedGraphToBigWig):

invalid unsigned integer: "1.35e+08"

Perhaps any difference below 0.01 (or some other threshold) should be set to 0?

— Reply to this email directly or view it on GitHubhttps://github.com/sartorlab/methylSig/issues/3.

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rcavalcante commented 9 years ago

Fixed with commit e153b3f6cc02761ff6f2515876e880aca8225058 in devel.