Description Details Value Slots Author(s) See Also

`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.

The positions in `marker.pos`

and `exp.pos`

matrix should be in the same units (e.g., base pair, kb, or cM).

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.

`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.

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

`trigger.build`

, `trigger.link`

, `trigger.mlink`

, `trigger.eigenR2`

, `trigger.net`

and `trigger.trait`

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