trigger-class {trigger} | R Documentation

## A class to store and analyze data for Transcriptional Regulation Inference from Genetics of Gene ExpRession

### Description

`trigger` is a class of objects to store and analyze data for Integrative Genomic Analysis. Use `trigger.build` to generate new objects of the class from input data.

### Details

The positions in `marker.pos` and `exp.pos` matrix should be in the same units (e.g., base pair, kb, or cM).

### Value

An object of S4 class `trigger` containing the marker genotype matrix (a matrix of 1,2 for haploid genotypes, or 1,2,3 for diploid genotypes), expression matrix, marker position matrix and gene/trait position matrix with ordered coordinates in respective slots. Use `slot(objectname, varname)` to retrieve individual variables from the object . Use `print` to see the first 10 rows and columns of the expression and marker matrix.

### Slots

`exp`:

  A numeric matrix with `m` rows and `n` columns, containing the gene expression (or intermediate trait) data.

`exp.pos`:

  A matrix with `m` rows and 3 columns containing the chromosome number, gene start and gene end for all the genes in the gene expression matrix. The rows of `exp.pos` should match those of `exp`.

`marker`:

  A matrix with `p` rows and `n` columns, containing genotyping information.

`marker.pos`:

  A matrix with `p` rows and 2 columns containing the chromosome number and SNP position for all the genes in the gene expression matrix. The rows of `exp.pos` should match those of `exp`.

`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.

`mlink`:

  A list containing the results of Multi-locus linkage analysis. See `trigger.mlink` for details.

`eqtl.R2`:

  A vector containing the proportion of genome-wide variation explained by each observed locus (eQTL).See `trigger.eigenR2` for details.

`loc.obj`:

  A list containing the results of local-linkage probability estimation. See `trigger.loclink` for details.

### 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

`trigger.build`, `trigger.link`, `trigger.mlink`, `trigger.eigenR2`, `trigger.net` and `trigger.trait`

[Package trigger version 1.28.0 Index]