FC.Anal: Fold change
In flajole/MApckg: R package of MetaboAnalyst functions

Description Usage Arguments Details Value See Also

Fold change (FC) analysis is to compare the absolute value change between two group means. Since column-wise normalization (i.e. log transformation, mean-centering) will significantly change the absolute values, FC is calculated as the ratio between two group means using data before column-wise normalization was applied.

1 2	FC.Anal(dataSet, analSet, fcthresh = 2, percent.thresh = 0.75, cmpType = 0)

`dataSet`	List, data set object generated by `MS_to_MA` function.
`analSet`	List, containing the results of statistical analysis (can be just an empty list).
`fcthresh`	Fold-change threshold.
`percent.thresh`	Sig. count threshold (for paired data only).
`cmpType`	Comparison type. If equal `0` then group 1 is compared against group 2. Otherwise, vice versa.

For paired analysis, the program first counts the number of pairs with consistent change above the given FC threshold. If this number exceeds a given count threshold, the variable will be reported as significant. Writes an output file "fold_change.csv".

Native analSet with one added $fc element consisting of:

$paired - are data paired or not
$raw.thresh - value of fcthresh argument
$max.thresh - upper log-threshold of fold change
$min.thresh - lower log-threshold of fold change
$fc.all - fold changes of all features
$fc.mat - matrix of fold changes (for paired data only)
$fc.log - log2 of fold changes (for unpaired data only)
$inx.up - logical vector of increasing features (for paired data only)
$inx.down - logical vector of decreasing features (for paired data only)
$inx.imp - logical vector of features with significant difference (for unpaired data only)
$sig.mat - data frame of significant features