Description Usage Arguments Value Examples
Subset the output of scan1()
by chromosome or column
1 2 3 4 |
x |
An object of class |
map |
A list of vectors of marker positions, as produced by
|
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 |
Object of same form as input, but subset by chromosome and/or column.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | ## Not run:
# load qtl2geno package for data and genoprob calculation
library(qtl2geno)
# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))
# 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")
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.