Description Usage Arguments Details Value References Examples
View source: R/summary_scan1perm.R
Summarize permutation test results from scan1perm()
, as significance thresholds.
1 2 3 4 | summary_scan1perm(object, alpha = 0.05)
## S3 method for class 'scan1perm'
summary(object, alpha = 0.05, ...)
|
object |
Output of |
alpha |
Vector of significance levels |
... |
Ignored |
In the case of X-chromosome-specific permutations (when
scan1perm()
was run with perm_Xsp=TRUE
, we
follow the approach of Broman et al. (2006) to get separate
thresholds for the autosomes and X chromosome, using
Let L_A and L_X be total the genetic lengths of the autosomes and X chromosome, respectively, and let L_T = L_A + L_X Then in place of alpha, we use
alpha_A = 1 - (1 - alpha)^(L_A/L_T)
as the significance level for the autosomes and
alpha_x = 1 - (1 - alpha)^(LX/LT)
as the significance level for the X chromosome.
An object of class summary.scan1perm
. If
scan1perm()
was run with perm_Xsp=FALSE
, this is
a single matrix of significance thresholds, with rows being
signicance levels and columns being the columns in the input. If
scan1perm()
was run with perm_Xsp=TRUE
, this is
a list of two matrices, with the significance thresholds for the
autosomes and X chromosome, respectively.
The result has an attribute "n_perm"
that has the numbers of
permutation replicates (either a matrix or a list of two matrices).
Broman KW, Sen <c5><9a>, Owens SE, Manichaikul A, Southard-Smith EM, Churchill GA (2006) The X chromosome in quantitative trait locus mapping. Genetics 174:2151-2158
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 | # 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$covar)
Xcovar <- get_x_covar(iron)
# permutations with genome scan
## Not run:
operm <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar,
n_perm=1000, perm_Xsp=TRUE,
chr_lengths=chr_lengths(iron$gmap))
## End(Not run)
summary(operm, alpha=c(0.20, 0.05))
|
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