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Fold change calculation

Source: R/utils-exported.R
getFCParams.Rd

Fold change calculation

Usage

getFCParams(replicates, ...)

Arguments

replicates

A character vector with the names of the two replicates to be compared.

...

Optional named arguments that override defaults.

Details

Fold change calculation can be used to easily identify significant changes between replicates. The calculation process is configured through a parameter list, which can be constructed with the getFCParams function. The parameter list has the following entries:

  • replicates the name of the two replicates to compare (taken from the replicates argument to getFCParams).

  • thresholdFC: the threshold log FC for a feature group to be classified as increasing/decreasing.

  • thresholdPV: the threshold log P for a feature group to be significantly different.

  • zeroMethod,zeroValue: how to handle zero values when calculating the FC: add adds an offset to zero values, "fixed" sets zero values to a fixed number and "omit" removes zero data. The number that is added/set by the former two options is defined by zeroValue.

  • PVTestFunc: a function that is used to calculate P values (usually using t.test).

  • PVAdjFunc: a function that is used to adjust P values (usually using p.adjust)

See also

featureGroups-class and feature-plotting

Author

The code to calculate and plot Fold change data was created by Bas van de Velde.