assoc.plot: Plot association mapping results.

Description

After performing association mapping using assoc.map, plot the mapping statistic along with genes in the QTL interval.

Usage

assoc.plot(results,  mgi.file = "ftp://ftp.jax.org/SNPtools/genes/MGI.20130703.sorted.txt.gz",  highlight, highlight.col = "red", thr, show.sdps = FALSE, ...)

Arguments

results

Data.frame containing output from assoc.map.

mgi.file

Character string containing the full path to a Tabix indexed file of gene locations. Default points to a version of the MGI genome feature file.

highlight

Character vector containing gene symbols to highlight in the plot.

highlight.col

Vector of colors to use when highlighting genes.

thr

Numeric value above which data points should be colored red and SNPs with these points returned.

show.sdps

Logical value (default = FALSE) that is TRUE if the strain distribution pattern (SDP) for the SNPs should be shown. When used with thr, only plots the founder SDPs for SNPs above thr.

...

Additional arguments passed to plot.

Value

A plot with the mapping statistic in the top panel and genes in the lower panel. If thr is not missing, then filter the SNPs in the results argument and return only those with a mapping statistic greater than thr.

Details

Given the output from assoc.map, plot the LOD or difference in BIC values across the QTL interval in the top panel. Plot the genes in the interval in the lower panel. Make sure to use Sanger SNP and MGI feature files that are on the same genome build.

Examples

Run this code

  ## Not run:  
#     results = assoc.map(pheno = pheno, pheno.col = 1, probs = probs, K = K, addcovar = addcovar, 
# 	snps = snps, chr = 1, start = 40, end = 45)
#     assoc.plot(results, thr = 3, show.sdps = TRUE)
#   ## End(Not run)