convert_to_scan1_output: Convert 'scan_multi_oneqtl' output of 'qtl2::scan1' output

In fboehm/qtl2pleio: Testing Pleiotropy in Multiparental Populations

Description

We convert output of 'scan_multi_oneqtl' into format outputted by 'qtl2::scan1'.

Usage

convert_to_scan1_output(sm_output, trait_name)

Arguments

sm_output	tibble output from scan_multi_oneqtl for one chromosome only
trait_name	character vector (of length one) specifying the trait names

Value

object of class 'scan1'

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)

# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- qtl2::get_x_covar(iron)

aprobs <- qtl2::genoprob_to_alleleprob(probs)
sm_out <- scan_multi_oneqtl(probs = aprobs, pheno = pheno)
sm_to_s1 <- convert_to_scan1_output(sm_out[[1]], trait_name = "tr1and2")

# 95% Bayes credible interval for QTL on chr 7, first phenotype
qtl2::bayes_int(sm_to_s1, map)

fboehm/qtl2pleio documentation built on July 17, 2021, 11:34 p.m.