get_effects {qtl2pleio}

Extract founder allele effects at a single marker from output of qtl2::scan1coef

Description

Extract founder allele effects at a single marker from output of qtl2::scan1coef

Usage

get_effects(marker_index, allele_effects_matrix, map, columns = 1:8)

Arguments

marker_index

an integer indicating where in the 'map' object the peak position (or position of interest) is located

allele_effects_matrix

output of 'qtl2::scan1coef' for a single chromosome

map

a map object for the chromosome of interest

columns

which columns to choose within the 'allele_effects_matrix'. Default is 1:8 to reflect 8 founder alleles of Diversity Outbred mice

Value

a vector of 8 founder allele effects at a single marker

a vector of founder allele effects at a single marker

Examples

# set up allele effects matrix
ae <- matrix(dat = rnorm(100 * 8), ncol = 8, nrow = 100)
ae[, 8] <- - rowSums(ae[, 1:7])
colnames(ae) <- LETTERS[1:8]
rownames(ae) <- paste0(1, "_", 1:100)
# set up map
map <- 1:100
names(map) <- rownames(ae)
# call get_effects
get_effects(marker_index = 15, allele_effects_matrix = ae, map = map)