trigger.mlink-methods {trigger} | R Documentation |
Multi-locus linkage (epistasis) analysis.
## S4 method for signature 'trigger' trigger.mlink(triggerobj, prob.cut = 0.9, gender = NULL, idx = NULL, B = 5, seed = 123)
triggerobj |
An object of class |
prob.cut |
Probability threshold for primary linkage. |
gender |
Optional. When computing linkage statistics involving markers on sex chromosome, |
idx |
The indices for genes to be computed for multi-locus linkage. |
B |
The number of null iterations to perform. |
seed |
Optional. A numeric seed for reproducible results. |
When data set is large, one can the option idx
to select a subset of genes in each computation and parallel-computes the genome-wide multi-locus linkage. Since the function computes the linkage probability by borrowing information across genes, at least more than 100 genes should be selected in applying this function. If idx=NULL
, all the genes in the input data will be computed for multi-locus linkage.
The current version of the function could only compute two-locus joint linkage (epistasis).
An updated object of class trigger
containing a slot trigger.mlink
with fields:
qtl |
The major and secondary QTLs for each selected gene. |
prob |
The posterior probability of linkage for major QTL, secondary QTL, and the joint posterior probability of multi-locus linkage. |
qvalue |
Q-value estimates for joint multi-locus linkage probabilities. |
Use slot(triggerobj, "mlink")
to retrieve the list.
Lin S. Chen lschen.stat@gmail.com, Dipen P. Sangurdekar dps@genomics.princeton.edu and John D. Storey jstorey@princeton.edu
Brem R.B., Storey J.D., Whittle J., and Kruglyak L. (2005) Genetic interactions between polymorphisms that affect gene expression in yeast. Nature, 436(7051): 701–703.
Storey J.D., Akey J.M., and Kruglyak L. (2005) Multiple locus linkage analysis of genomewide expression in yeast. PLoS Biology, 3(8): 1380–1390.
trigger.link and plot
## Not run: data(yeast) attach(yeast) triggerobj <- trigger.build(marker = marker,exp = exp, marker.pos = marker.pos, exp.pos = exp.pos) ## Genome-wide multiple locus linkage analysis triggerobj <- trigger.mlink(triggerobj, B = 10, idx = NULL, seed = 123) plot(triggerobj, type = "trigger.mlink", qcut=0.1, bin.size=NULL) mlink = slot(triggerobj, "trigger.mlink") detach(yeast) ## End(Not run)