trigger-eigenR2: Estimate the proportion of genome-wide variation explained by...
In trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description Usage Arguments Value Author(s) References See Also Examples

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

1 2	## S4 method for signature 'trigger' trigger.eigenR2(triggerobj, adjust = FALSE, meanR2 = FALSE)

`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.

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.

Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu

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

plot

## 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)