allele1: Allele plot for SNPs, alleles and allele pairs

In byandell/qtl2pattern: Pattern Support for 'qtl2' Package

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 calc_genoprob
phe_df	data frame with one phenotype
cov_mx	covariate matrix
map	Genome map (required if scan1_object present).
K_chr	kinship matrix
patterns	data frame of pattern information
alt	Haplotype allele letter(s) for alternative to reference.
blups	Create BLUPs if TRUE
...	Other parameters ignored.
object	Object of class allele1.
scan1_object	Optional object of class scan1 to find peak.
pos	Genome position in Mbp (supercedes scan1_object).
trim	If TRUE, trim extreme alleles.
legend.position	Legend position (default is "none").

Value

Table with allele effects across sources.

object of class ggplot

byandell/qtl2pattern documentation built on Nov. 9, 2023, 7:57 p.m.