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

In StoreyLab/trigger-devel: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

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 [e-mail], Dipen P. Sangurdekar [e-mail] and John D. Storey [e-mail]

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)

StoreyLab/trigger-devel documentation built on May 9, 2019, 3:11 p.m.