Description Usage Arguments Value Author(s) References See Also Examples
Automatic function that performs REMIM algorithm using score statistics.
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data |
an object of class |
pheno.col |
a numeric vector with the phenotype columns to be analyzed or printed; if |
w.size |
the window size (in centiMorgans) to avoid on either side of QTL already in the model when looking for a new QTL, e.g. 15 (default). |
sig.fwd |
the desired score-based significance level for forward search, e.g. 0.01 (default). |
sig.bwd |
the desired score-based significance level for backward elimination, e.g. 0.001 (default). |
score.null |
an object of class |
d.sint |
a d value to subtract from logarithm of p-value (LOP-d) for support interval calculation, e.g. d=1.5 (default) represents approximate 95% support interval. |
polygenes |
if |
n.clusters |
number of parallel processes to spawn. |
n.rounds |
number of search rounds; if |
plot |
a suffix for the file's name containing plots of every algorithm step, e.g. "remim"; if |
verbose |
if |
x |
an object of class |
sint |
whether |
... |
currently ignored |
An object of class qtlpoly.remim
which contains a list of results
for each trait with the following components:
pheno.col |
a phenotype column number. |
stat |
a vector containing values from score statistics. |
pval |
a vector containing p-values from score statistics. |
qtls |
a data frame with information from the mapped QTL. |
lower |
a data frame with information from the lower support interval of mapped QTL. |
upper |
a data frame with information from the upper support interval of mapped QTL. |
Guilherme da Silva Pereira, gdasilv@ncsu.edu
Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152 (3): 1203–16.
Pereira GS, Gemenet DC, Mollinari M, Olukolu BA, Wood JC, Mosquera V, Gruneberg WJ, Khan A, Buell CR, Yencho GC, Zeng ZB (2020) Multiple QTL mapping in autopolyploids: a random-effect model approach with application in a hexaploid sweetpotato full-sib population, Genetics 215 (3): 579-595. doi: 10.1534/genetics.120.303080.
Qu L, Guennel T, Marshall SL (2013) Linear score tests for variance components in linear mixed models and applications to genetic association studies. Biometrics 69 (4): 883–92.
Zou F, Fine JP, Hu J, Lin DY (2004) An efficient resampling method for assessing genome-wide statistical significance in mapping quantitative trait loci. Genetics 168 (4): 2307-16. doi: 10.1534/genetics.104.031427
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# Estimate conditional probabilities using mappoly package
library(mappoly)
library(qtlpoly)
genoprob4x = lapply(maps4x[c(5)], calc_genoprob)
data = read_data(ploidy = 4, geno.prob = genoprob4x, pheno = pheno4x, step = 1)
# Search for QTL
remim.mod = remim(data = data, pheno.col = 1, w.size = 15, sig.fwd = 0.0011493379,
sig.bwd = 0.0002284465, d.sint = 1.5, n.clusters = 1)
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