listof_scan1coef: List of scan1coef objects

In qtl2ggplot: Data Visualization for QTL Experiments

List of scan1coef objects

Description

Create a list of scan1coef objects using scan1coef.

Summary of object of class listof_scan1coef, which is a list of objects of class scan1coef.

Summary of object of class listof_scan1coef, which is a list of objects of class scan1coef.

Subset of object of class listof_scan1coef, which is a list of objects of class scan1coef.

Usage

listof_scan1coef(
  probs,
  phe,
  K = NULL,
  covar = NULL,
  blups = FALSE,
  center = FALSE,
  ...
)

summary_listof_scan1coef(
  object,
  scan1_object,
  map,
  coef_names = dimnames(object[[1]])[[2]],
  center = TRUE,
  ...
)

## S3 method for class 'listof_scan1coef'
summary(object, ...)

summary_scan1coef(object, scan1_object, map, ...)

## S3 method for class 'scan1coef'
summary(object, ...)

subset_listof_scan1coef(x, elements, ...)

## S3 method for class 'listof_scan1coef'
subset(x, ...)

## S3 method for class 'listof_scan1coef'
x[...]

Arguments

probs	genotype probabilities object for one chromosome from calc_genoprob
phe	data frame of phenotypes
K	list of length 1 with kinship matrix
covar	matrix of covariates
blups	Create BLUPs if TRUE
center	center coefficients if TRUE
...	ignored
object	object of class listof_scan1coef
scan1_object	object from scan1
map	A list of vectors of marker positions, as produced by insert_pseudomarkers.
coef_names	names of effect coefficients (default is all coefficient names)
x	object of class listof_scan1coef
elements	indexes or names of list elements in x

Value

object of class listof_scan1coef

Author(s)

Brian S Yandell, [e-mail]

Examples

# read data
iron <- qtl2::read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# insert pseudomarkers into map
map <- qtl2::insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- qtl2::calc_genoprob(iron, map, error_prob=0.002)

# Ensure that covariates have names attribute
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)

# Calculate scan1coef on all phenotypes,
# returning a list of \code{\link{scan1coef}} objects
out <- listof_scan1coef(probs[,7], iron$pheno, addcovar = covar, center = TRUE)

# Plot coefficients for all phenotypes
ggplot2::autoplot(out, map[7], columns = 1:3)

# Summary of coefficients at scan peak
scan_pr <- qtl2::scan1(probs[,7], iron$pheno)
summary(out, scan_pr, map[7])

qtl2ggplot documentation built on March 31, 2023, 6:06 p.m.