trigger-link: Genomewide eQTL analysis

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

Description

A method of class trigger for genomewide Expression-trait QTL analysis. This function estimates the linkage statistic and parametric p-value for each gene expression to every locus in the genome.

Usage

  ## S4 method for signature 'trigger'
trigger.link(triggerobj, gender = NULL, norm = TRUE)

Arguments

triggerobj	An object of class trigger.
gender	Optional. When computing linkage statistics involving markers on sex chromosome, gender of each sample should be specified.
norm	Logical. If TRUE, each row of expression matrix exp in the triggerobj will be transformed to follow a standard normal distribution, based on the rank of value.

Value

An updated object of class trigger containing slots:

stat	A matrix of pair-wise likelihood ratio statistics for linkage analysis, with genes in rows and markers in columns.
pvalue	A matrix of parametric pvalues corresponding to statistics in the stat matrix.

Use slot(triggerobj, "stat") and slot(triggerobj, "pvalue") to retrieve the values.

Author(s)

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

See Also

plot and trigger.mlink

Examples

## Not run: 
  data(yeast)
  attach(yeast)
  triggerobj <- trigger.build(marker = marker, exp = exp, 
				marker.pos = marker.pos, exp.pos = exp.pos)
  triggerobj <- trigger.link(triggerobj, gender = NULL, norm = TRUE)
  plot(triggerobj,type = "link", cutoff = 1e-5)
  stat = slot(triggerobj, "stat"); pvalue = slot(triggerobj, "pvalue")
  detach(yeast)


## End(Not run)

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