Find position with maximum LOD score
Return data frame with the positions having maximum LOD score for a particular LOD score column
max_scan1( scan1_output, map = NULL, lodcolumn = 1, chr = NULL, na.rm = TRUE, ... ) ## S3 method for class 'scan1' max(scan1_output, map = NULL, lodcolumn = 1, chr = NULL, na.rm = TRUE, ...)
scan1_output |
An object of class |
map |
A list of vectors of marker positions, as produced by
|
lodcolumn |
An integer or character string indicating the LOD
score column, either as a numeric index or column name.
If |
chr |
Optional vector of chromosomes to consider. |
na.rm |
Ignored (take to be TRUE) |
... |
Ignored |
If map is NULL, the genome-wide maximum LOD score for the selected column is returned.
If also lodcolumn is NULL, you get a vector with the maximum LOD for each column.
If map is provided, the return value is a data.frame with three columns: chr, pos, and lod score.
But if lodcolumn is NULL, you get the maximum for each lod score column, in the format provided by
find_peaks(), so a data.frame with five columns: lodindex, lodcolumn, chr, pos, and lod.
# 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)
# maximum of first column
max(out, map)
# maximum of spleen column
max(out, map, lodcolumn="spleen")
# maximum of first column on chr 2
max(out, map, chr="2")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.