makePSN_NamedMatrix param clash

BaderLab / netDx

R package with netDx software and data for examples

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makePSN_NamedMatrix param clash #32

Closed shraddhapai closed 4 years ago

shraddhapai commented 7 years ago

If custom function is provided and writeProfiles=TRUE, throw error. Message should specify when to use each and not to use both together.

shraddhapai commented 7 years ago

Just updated this code. Minor test, hopefully fine. Close this comment after we've tested it.

shraddhapai commented 7 years ago

writeProfiles=FALSE results in use of Pearson correlation metric with na.omit(). However, writeProfiles=TRUE calls Pearson corr via ProfileToNetworkDriver which does NOT have na.omit(). behaviour of the two should be consistent. Maybe add a removeNA flag which is set to FALSE by default so that Pearson corr isn't quietly removing NAs.