mouse {CVR}

Data sets for the mouse body weight example

Description

A list of 3 data frames that contains the genotype, gene expression and body-mass index of 294 mice. The data is already screened for quality control. For the raw data see the links below. For more details see the reference.

Usage

mouse

Format

A list of 3 data frames:

geno

Mouse genotype. A data frame of 294 rows and 163 columns.

expr

Mouse gene expression. A data frame of 294 rows and 215 columns.

bmi

Mouse body-mass index. A data frame of 294 rows and 1 column.

Source

Mouse genotype: http://www.genetics.org/cgi/content/full/genetics.110.116087/DC1 Mouse gene expression: ftp://ftp.ncbi.nlm.nih.gov/pub/geo/DATA/SeriesMatrix/GSE2814/ Mouse body-mass index: http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/MouseWeight/.

References

Chongliang Luo, Jin Liu, Dipak D. Dey and Kun Chen (2016) Canonical variate regression. Biostatistics, doi: 10.1093/biostatistics/kxw001.

Examples

############## Mouse body weight example ######################
data(mouse)
expr <- scale(as.matrix(mouse$expr))
geno <- scale(as.matrix(mouse$geno))
bmi <- as.matrix(mouse$bmi)
mouse.X <- list(X1 = expr, X2 = geno)
## Not run: 
 mouse.cvr <- CVR(bmi, mouse.X, rankseq = 2, etaseq = 0.04, family = "g", penalty = "L1")
 plot(mouse.cvr)
 plot(expr %*% mouse.cvr$solution$W[[1]][, 2], geno %*% mouse.cvr$solution$W[[2]][, 2])
 cor(expr %*% mouse.cvr$solution$W[[1]], geno %*% mouse.cvr$solution$W[[2]]) 
 
## End(Not run)