plot_haplofreq: Plot and filter markers based on haplotype frequency vs...
In jendelman/MapRtools: Tools for genetic mapping
View source: R/plot_haplofreq.R
plot_haplofreq R Documentation
Plot and filter markers based on haplotype frequency vs position
Description
Plot and filter markers based on haplotype frequency vs position
Usage
plot_haplofreq(geno, thresh = 0.1, span = 0.3)
Arguments
geno
haplotype dosage matrix (markers x indiv)
thresh
threshold for removing markers (see Details)
span
parameter to control degree of smoothing for spline (higher = less smooth)
Details
This functions works for mapping populations derived from two inbred founders. The geno matrix must be coded based on the dosage (0,1,2) of one founder haplotype.
Markers are removed if their residual to the fitted spline exceeds thresh. Markers are assumed to be ordered. Function designed to be used for one chromosome.
Value
List containing
- outliers
index of outlier markers
- plot
ggplot2 variable
jendelman/MapRtools documentation built on April 12, 2025, 12:46 p.m.
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View source: R/plot_haplofreq.R
| plot_haplofreq | R Documentation |
Plot and filter markers based on haplotype frequency vs position
Description
Plot and filter markers based on haplotype frequency vs position
Usage
plot_haplofreq(geno, thresh = 0.1, span = 0.3)
Arguments
geno |
haplotype dosage matrix (markers x indiv) |
thresh |
threshold for removing markers (see Details) |
span |
parameter to control degree of smoothing for spline (higher = less smooth) |
Details
This functions works for mapping populations derived from two inbred founders. The geno matrix must be coded based on the dosage (0,1,2) of one founder haplotype.
Markers are removed if their residual to the fitted spline exceeds thresh. Markers are assumed to be ordered. Function designed to be used for one chromosome.
Value
List containing
- outliers
index of outlier markers
- plot
ggplot2 variable
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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