dataf.geneexp: Gene Expression Profile Data

In ddalpha: Depth-Based Classification and Calculation of Data Depth

Gene Expression Profile Data

Description

A subet of the Drosophila life cycle gene expression data of Arbeitman et al. (2002). The original data set contains 77 gene expression profiles during 58 sequential time points from the embryonic, larval, and pupal periods of the life cycle. The gene expression levels were obtained by a cDNA microarray experiment.

Usage

dataf.geneexp()

Format

The functional data as a data structure.

dataf

The functional data as a list of objects. Each object is characterized by two coordinates.

args

Time - a numeric vector of time periods

vals

Gene Expression Level - a numeric vector

labels

Biological classifications identified in Arbeitman et al.(2002) (1 = transient early zygotic genes; 2 = muscle-specific genes; 3 = eye-specific genes. )

Source

Chiou, J.-M. and Li, P.-L. Functional clustering and identifying substructures of longitudinal data, J. R. Statist. Soc. B, Volume 69 (2007), 679-699

Arbeitman, M.N., Furlong, E.E.M., Imam,F., Johnson, E., Null,B.H., Baker,B.S., Krasnow, M.A., Scott,M.P., Davis,R.W. and White,K.P. (2002) Gene expression during the life cycle of Drosophila melanogaster. Science, 297, 2270-2274.

See Also

dataf.* for other functional data sets

plot.functional for building plots of functional data

Examples

## load the dataset
dataf = dataf.geneexp()

## view the classes
unique(dataf$labels)

## access the 5th point of the 2nd object
dataf$dataf[[2]]$args[5]
dataf$dataf[[2]]$vals[5]

## plot the data
## Not run: 
labels = unlist(dataf$labels)
plot(dataf, 
  xlab="Time", ylab="Gene Expression Level", 
  main=paste0("Gene Expression:  1 red (", sum(labels == 1), "), ", 
            "2 green (", sum(labels == 2), "), ", 
            "3 blue (", sum(labels == 3), ")"),
  colors = c("red", "green", "blue"))

## End(Not run)

ddalpha documentation built on Oct. 1, 2024, 1:07 a.m.