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