qtl2 (version 0.32)

subset_scan1: Subset scan1 output

Description

Subset the output of scan1() by chromosome or column

Usage

subset_scan1(x, map = NULL, chr = NULL, lodcolumn = NULL, ...)
# S3 method for scan1
subset(x, map = NULL, chr = NULL, lodcolumn = NULL, ...)

Value

Object of class "scan1", like the input, but subset by chromosome and/or column. See scan1().

Arguments

x

An object of class "scan1" as returned by scan1().

map

A list of vectors of marker positions, as produced by insert_pseudomarkers().

chr

Vector of chromosomes.

lodcolumn

Vector of integers or character strings indicating the LOD score columns, either as a numeric indexes or column names.

...

Ignored

Examples

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

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

# calculate genotype probabilities
probs <- 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 <- get_x_covar(iron)

# perform genome scan
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)

# pull out chromosome 8
out_c8 <- subset(out, map, chr="8")

# just the second column on chromosome 2
out_c2_spleen <- subset(out, map, "2", "spleen")

# all positions, but just the "liver" column
out_spleen <- subset(out, map, lodcolumn="spleen")