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radmeth adjust outputs -1-1 in 7th field #10

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guilhermesena1 opened this issue Jul 7, 2022 · 0 comments
Open

radmeth adjust outputs -1-1 in 7th field #10

guilhermesena1 opened this issue Jul 7, 2022 · 0 comments

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@guilhermesena1
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guilhermesena1 commented Jul 7, 2022

When there average methylation difference in radmeth is zero from the C/(C+T) estimates of each case-control, radmeth adjust outputs lines like this:

chr1    10866   +       CpG     -1      -1      -1-1    3       3       25      25

This causes issues to filter significant CpGs. For example we often do (and the documentation suggests on page 16) that we filter significant FDR-corrected CpGs using

awk '$7 <= 0.01' input-adjusted.radmeth >output-significant.radmeth

This does not filter these lines with zero average difference. Should the p-values for these lines be 1 instead?

@guilhermesena1 guilhermesena1 changed the title radmeth merge outputs -1-1 in 7th field radmeth adjust outputs -1-1 in 7th field Jul 7, 2022
@andrewdavidsmith andrewdavidsmith transferred this issue from smithlabcode/methpipe Oct 16, 2022
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