getFCParams: Fold change calculation

In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis

Fold change calculation

Description

Fold change calculation

Usage

getFCParams(rGroups, ...)

Arguments

rGroups	A character vector with the names of the two replicate groups to be compared.
...	Optional named arguments that override defaults.

Details

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

• rGroups the name of the two replicate groups to compare (taken from the rGroups 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)

Author(s)

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

See Also

featureGroups-class and feature-plotting

rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.