assoc.plot: Plot association mapping results.

In dmgatti/DOQTL: Genotyping and QTL Mapping in DO Mice

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.

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.

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.

Author(s)

Daniel Gatti

See Also

assoc.map

Examples

  ## 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)

dmgatti/DOQTL documentation built on April 7, 2024, 10:35 p.m.