Description Usage Arguments Value Author(s)
Perform GWAS using the FarmCPU model.
1 2 3 4 5 6 | farmcpu(Y, GD, GM, CV = NULL, GP = NULL, method.sub = "reward",
method.sub.final = "reward", method.bin = "static",
bin.size = c(5e+05, 5e+06, 5e+07), bin.selection = seq(10, 100, 10),
memo = NULL, Prior = NULL, ncores.glm = 1, maxLoop = 10,
converge = 1, iteration.output = FALSE, p.threshold = NA,
ncores.reml = 1, threshold = 0.7)
|
Y |
A dataframe with two columns: a character column of sample names and a numeric column of phenotypic values. This dataframe may contain missing values. |
GD |
A |
GM |
A dataframe with three columns: a character column of sample names, a numeric column of chromosomes, and a numeric column of base-pair positions. |
CV |
An optional numeric matrix of covariates. |
GP |
A numeric vector of p-values to select pseudo-QTNs before single-marker regression in the first iteration. |
method.sub |
Character string indicating the method used to substitute
p-values for pseudo-QTNs. One of |
method.sub.final |
Character string indicating the method used to substitute p-values for pseudo-QTNs on the final iteration. |
method.bin |
Character string indicating the method used to select
pseudo-QTNs. One of |
bin.size |
A numeric vector specifying bin sizes in base-pairs for pseudo-QTN selection. |
bin.selection |
Numeric vector of numbers of pseudo-QTNs to select. |
memo |
Character string added to file names. |
Prior |
A dataframe with the same format as |
ncores.glm |
Integer scalar number of cores to use for single-marker regression. |
maxLoop |
Integer scalar maximum number of iterations to perform. |
converge |
Numeric scalar such that |
iteration.output |
Logical scalar. Whether to include the output of each iteration or not. |
p.threshold |
Numeric scalar. P-value threshold for inclusion of pseudo-QTNs in the model on the first iteration. Defaults to a 0.01 Bonferroni correction. |
ncores.reml |
Integer scalar number of cores to use for pseudo-QTN selection. |
threshold |
Numeric scalar maximum correlation allowed between pseudo-QTNs. |
A list. If iteration.output = FALSE
, the list has one element.
Otherwise, the list additionally has one element for each iteration. Each
element has one required element and one optional element. The required
element is a dataframe called GWAS
with seven columns: the marker
ID, the chromosome, the base-pair position, the marker p-value, the effect
estimate, the standard error, and the t-statistic. If there are
user-specified covariates, the results list contains a matrix called
CV
that contains the effect estimates for the covariates.
Xiaolei Liu
Zhiwu Zhang
Aaron Kusmec
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