
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.
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
:m
rows and n
columns, containing the gene expression (or intermediate trait) data.exp.pos
: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
:p
rows and n
columns, containing genotyping information.marker.pos
: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
:pvalue
:stat
matrix.mlink
:trigger.mlink
for details.eqtl.R2
:trigger.eigenR2
for details.loc.obj
:trigger.loclink
for details.marker.pos
and exp.pos
matrix should be in the same units (e.g., base pair, kb, or cM).
trigger.build
, trigger.link
, trigger.mlink
, trigger.eigenR2
, trigger.net
and trigger.trait