fibroblast: Fibroblast Cell Line dataset

In cumSeg: Change Point Detection in Genomic Sequences

Description

Genomic sequences of 15 fibroblast cell lines.

Usage

data(fibroblast)

Format

A data frame with 2462 observations on the following 11 variables.

Chromosome

a numeric vector to identify the chromosome

Genome.Order

a numeric vector meaning the genome index

gm05296

cell line GM05296

gm03563

cell line GM03563

gm01535

cell line GM01535

gm07081

cell line GM07081

gm01750

cell line GM01750

gm03134

cell line GM03134

gm13330

cell line GM13330

gm13031

cell line GM13031

gm01524

cell line GM01524

Details

Data come from a single experiments on 15 fibroblast cell lines with each array containing over 2000 (mapped) BACs spotted in triplicate. The variable in the dataset is the normalized average of the log base 2 test over reference ratio.

References

Snijders, A. M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A. K., Huey, B., Kimura, K. et al., (2001). Assembly of microarrays for genome-wide measurement of DNA copy number. Nature Genetics 29, 263-264.

Examples

## Not run: 
data(fibroblast)
#select chromosome 1
z<-na.omit(fibroblast$gm03563[fibroblast$Chromosome==1]) 
o<-jumpoints(z,k=30,output="3")
plot(z)
plot(o,add=TRUE,y=FALSE,col=4)

## End(Not run)

Example output

Loading required package: lars
Loaded lars 1.2

cumSeg documentation built on July 17, 2020, 5:07 p.m.