trigger-build: Format the input data and create an Trigger object

In igbucur/trigger: Transcriptional Regulatory Inference from Genetics of Gene ExpRession

Description

This function takes high-dimensional expression data and genotype data with each of their position data in the genome and creates a trigger object for subsequent analysis.

Usage

  trigger.build(exp = exp,exp.pos = exp.pos, marker = marker, marker.pos = marker.pos)

Arguments

exp	A gene (or intermediate trait) by individual matrix of expression data.
exp.pos	A matrix containing the position information for genes (intermediate traits). The first column is the chromosome name of the gene. The second column is the starting coordinate of the gene, and the third column is the ending coordinate. Each row corresponds to one gene/trait in the exp matrix.
marker	A marker genotype by individual matrix.
marker.pos	A matrix containing the position information for markers. The first column is the chromosome name of the marker. We recommend to use integers for autosomal chromosomes and "X" for sex chromosome. The second column is the position of the marker on the chromosome. Each row corresponds to one marker in the marker matrix.

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.

Author(s)

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

See Also

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

Examples

## Not run: 
  data(yeast)
  attach(yeast)
  triggerobj <- trigger.build(marker = marker, exp = exp, 
                    marker.pos = marker.pos, exp.pos = exp.pos)
  print(triggerobj)
  
## End(Not run)

igbucur/trigger documentation built on Oct. 16, 2020, 1:57 a.m.