trigger.link-methods {trigger} | R Documentation

## Genomewide eQTL analysis

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

### 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)

[Package trigger version 1.26.0 Index]