effectplot {qtl}R Documentation

Plot phenotype means against genotypes at one or two markers.

Description

Plot the phenotype means for each group defined by the genotypes at one or two markers (or the values at a discrete covariate).

Usage

effectplot(cross, pheno.col=1, mname1, mark1, geno1, mname2, mark2,
           geno2, main, ylim, add.legend=TRUE)

Arguments

cross An object of class cross.
pheno.col Column number in the phenotype matrix which to be drawn in the plot.
mname1 Name for the first marker.
mark1 Genotype data for the first marker. If unspecified, genotypes will be taken from the data in the input cross object, using the name specified in mname1.
geno1 Names for the genotypes (or classes in a covariate).
mname2 Name for the second marker (optional).
mark2 Like mark1 (optional).
geno2 Names for the genotypes (or classes in a covariate).
main Optional figure title.
ylim Y-axis limits.
add.legend A logical value to indicate add legend or not.

Details

In the plot, the Y-axis is the phenotype. X-axis is the genotype for the first marker. In the case of one marker, there will be one line in the figure. In the case of two markers, the x-axis is for different genotypes of the second marker, and the first marker is represented by lines in different colors. Error bars are plotted at +/- 1 SE.

Value

A data.frame containing the phenotype means and standard deviations for each group.

Author(s)

Hao Wu, hao@jax.org; Karl W Broman, kbroman@jhsph.edu

See Also

plot.pxg, find.marker, effectscan

Examples

data(fake.f2)

# plot of genotype-specific phenotype means for 1 marker
mname <- find.marker(fake.f2, 1, 37) # marker D1M437
effectplot(fake.f2, pheno.col=1, mname1=mname)

# Plot of sex-specific phenotype means
sex <- fake.f2$pheno[,2]
effectplot(fake.f2, mname1="Sex", mark1=sex, geno1=c("F","M"))

# plot of genotype-specific phenotype means for 2 markers
mname1 <- find.marker(fake.f2, 1, 37) # marker D1M437
mname2 <- find.marker(fake.f2, 13, 24) # marker D13M254
effectplot(fake.f2, mname1=mname1, mname2=mname2)

# Plot of sex- and genotype-specific phenotype means 
mname <- find.marker(fake.f2, 13, 24) # marker D13M254
effectplot(fake.f2, mname1=mname, mname2="Sex",
           mark2=fake.f2$pheno$sex, geno2=c("F","M"))

# Same as above, switch role of sex and the marker
effectplot(fake.f2, mname1="Sex", mark1=fake.f2$pheno$sex,
           geno1=c("F","M"), mname2=mname)

# X chromosome marker
mname <- find.marker(fake.f2, "X", 14) # marker DXM66
effectplot(fake.f2, mname1=mname)

# Two markers, including one on the X
mname1 <- find.marker(fake.f2, 13, 24) # marker D13M254
mname2 <- find.marker(fake.f2, "X", 14) # marker DXM66
effectplot(fake.f2, mname1=mname1, mname2=mname2)

[Package qtl version 0.98-57 Index]