assoc.plot: Plot association mapping results.
In DOQTL: Genotyping and QTL Mapping in DO Mice

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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.

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.

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.

Daniel Gatti

assoc.map

  ## 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)