allele1 {qtl2pattern}

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