fourierscore: Calculation of the Fourier score

In cycle: Significance of periodic expression pattern in time-series data

Description

The function calculates fourier score for a chosen periodicity.

Usage

fourierscore(eset,T,times=seq_len(ncol(eset)))

Arguments

eset	object of the class “ExpressionSet”
T	length of chosen period
times	measurement times (with the index of the column as default)

Details

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.

Value

Fourier scores for all features (genes) of eset

Note

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.

Author(s)

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

References

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

Examples

# 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]])
}

Example output

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 

cycle documentation built on Nov. 8, 2020, 8:31 p.m.