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kevinblighe / EnhancedVolcano

Publication-ready volcano plots with enhanced colouring and labeling
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p-value or adjusted-p-value #44

Closed Homap closed 4 years ago

Homap commented 4 years ago

Hello,

Thank you for the fantastic package.

I was wondering whether the function uses p-values or adjusted p-values? Is adjusted p-value threshold determined by pLabellingCutoff argument?

Thank you again, Homa

kevinblighe commented 4 years ago

Hey Homa. The user can choose to plot nominal (un-adjusted) or adjusted p-values by selecting a different column name from the input results table.

The value of pLabellingCutoff will always be applied indiscriminately as: -log10(pLabellingCutoff) ...irrespective of the nature of the input p-values.

Homap commented 4 years ago

Thank you so much.

kevinblighe commented 4 years ago

Sure thing!