trigger.eigenR2-methods {trigger} | R Documentation

## 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

    	## S4 method for signature 'trigger'
    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.

### Author(s)

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

### 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)

[Package trigger version 1.26.0 Index]