Fold change calculation
getFCParams(replicates, ...)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)