allele1 {qtl2pattern} | R Documentation |
Allele plot for SNPs, alleles and allele pairs
Description
Create table of alleles for various model fits.
Plot alleles for haplotype, diplotype and top patterns and genome position.
Usage
allele1(
probD,
phe_df = NULL,
cov_mx = NULL,
map = NULL,
K_chr = NULL,
patterns = NULL,
alt = NULL,
blups = FALSE,
...
)
ggplot_allele1(
object,
scan1_object = NULL,
map = NULL,
pos = NULL,
trim = TRUE,
legend.position = "none",
...
)
## S3 method for class 'allele1'
autoplot(object, ...)
Arguments
probD |
object of class |
phe_df |
data frame with one phenotype |
cov_mx |
covariate matrix |
map |
Genome map (required if |
K_chr |
kinship matrix |
patterns |
data frame of pattern information |
alt |
Haplotype allele letter(s) for alternative to reference. |
blups |
Create BLUPs if |
... |
Other parameters ignored. |
object |
Object of class |
scan1_object |
Optional object of class |
pos |
Genome position in Mbp (supercedes |
trim |
If |
legend.position |
Legend position (default is |
Value
Table with allele effects across sources.
object of class ggplot
[Package qtl2pattern version 1.2.1 Index]