Description Usage Arguments Details Value Note Author(s) References Examples

The function calculates fourier score for a chosen periodicity.

1 | ```
fourierscore(eset,T,times=seq_len(ncol(eset)))
``` |

`eset` |
object of the class “ExpressionSet” |

`T` |
length of chosen period |

`times` |
measurement times (with the index of the column as default) |

The Fourier score can be used to detect periodic signals.
The closer a gene's expression follows a (possibly shifted) cosine curve of period T, the larger is the Fourier score. Mathematical details can be found in the given reference. The function `fourierscore`

calculates the Fourier scores for all features of an ExpressionSet object.

Fourier scores for all features (genes) of `eset`

Note that this function evaluates soley the `exprs`

matrix and
no information is used from the `phenoData`

. In particular,
the ordering of samples (arrays) is the same as the ordering
of the columns in the `exprs`

matrix. Also, replicated arrays in the
`exprs`

matrix are treated as independent
i.e. they should be averagered prior to analysis or placed into different
distinct “ExpressionSet” objects.

Matthias E. Futschik (http://www.cbme.ualg.pt/mfutschik_cbme.html)

Matthias E. Futschik and Hanspeter Herzel (2008) Are we overestimating the number of cell-cycling genes? The impact of background models on time series analysis, *Bioinformatics*, 24(8):1063-1069

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 | ```
# Data preprocessing
if (interactive()){
set.seed(1)
data(yeast) # loading the reduced CDC28 yeast set (from the Mfuzz package)
yeast <- yeast[1:600,] # for illustration
yeast <- filter.NA(yeast) # filters genes with more than 25% of the expression values missing
yeast <- fill.NA(yeast) # for illustration only; rather use knn method for
yeast <- standardise(yeast)
T.yeast <- 85 # cell cycle period (t=85min)
times.yeast <- pData(yeast)$time # time of measurements
F <- fourierscore(yeast,T = T.yeast, times= times.yeast)
# calculates the Fourier scores for yeast genes
# Plot highest scoring gene
plot(times.yeast,exprs(yeast)[order(-F)[1],],type="o",
xlab="Time",ylab="Expression",
main=featureNames(yeast)[order(-F)[1]])
# Plot lowest scoring gene
plot(times.yeast,exprs(yeast)[order(F)[1],],type="o",
xlab="Time",ylab="Expression",
main=featureNames(yeast)[order(F)[1]])
}
``` |

```
Loading required package: Mfuzz
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
setdiff, sort, table, tapply, union, unique, unsplit, which,
which.max, which.min
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Loading required package: e1071
Warning message:
no DISPLAY variable so Tk is not available
```

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