Subset scan1 output
Subset the output of scan1() by chromosome or column
subset_scan1(x, map = NULL, chr = NULL, lodcolumn = NULL, ...) ## S3 method for class 'scan1' subset(x, map = NULL, chr = NULL, lodcolumn = NULL, ...)
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 class "scan1", like the input, but subset by chromosome and/or column. See scan1().
# 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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.