trigger (version 1.18.0)

trigger.eigenR2-methods: Estimate the proportion of genome-wide variation explained by each eQTL

Description

Estimate eqtl-R2, the proportion of genome-wide variation explained by each eQTL and identify linkage hotspots.

Usage

"trigger.eigenR2"(triggerobj, adjust = FALSE, meanR2 = FALSE)

Arguments

triggerobj

An object of class trigger.

adjust

Logical. If TRUE, the estimated R-square for each locus will be adjusted for small sample size effect. Recommend to use when sample size is less than 100.

meanR2

Logical. If TRUE, the function computes the mean of R-squares of genome-wide gene expression for each locus.

Value

An updated object of class trigger with a slot loc.obj containing the proportion of genome-wide variation explained by each observed locus (eQTL). Use slot(triggerobj, "eigenR2") to retrieve the eqtl-R2 values as a vector.

References

Chen L.S. and Storey J.D. (2008) Eigen-R2 for dissecting variation in high-dimensional studies. Bioinformatics 24(19): 2260--2262.

See Also

plot

Examples

## Not run: 
#   data(yeast)
#   attach(yeast)
#   triggerobj <- trigger.build(marker = marker, exp = exp, 
# 			marker.pos = marker.pos, exp.pos = exp.pos)
#   triggerobj <- trigger.eigenR2(triggerobj, adjust = FALSE)
#   plot(triggerobj, type = "eigenR2")
#   eqtlR2 <- slot(triggerobj, "eigenR2")
#   detach(yeast)
# 
# ## End(Not run)