| VIFGC {GenABEL} | R Documentation |
This function estimates corrected statistic using genomic control for different models (recessive, dominant, additive etc.), using VIF. VIF coefficients are estimated by optimizing different error functions: regress, median and ks.test.
VIFGC(data, p, x, method = "regress", n,
index.filter = NULL, proportion = 1, clust = 0,
vart0 = 0, tmp = 0, CA = FALSE, p.table = 0,
plot = TRUE, lmax = NULL, color = "red", F = NULL,
K = NULL, type_of_plot = "plot", ladd = NULL)
data |
Input vector of Chi square statistic |
method |
Function of error to be optimized. Can be "regress", "median" or "ks.test" |
p |
Input vector of allele frequencies |
x |
Model of inheritance (0 for recessive,0.5 for additive, 1 for dominant, also it could be arbitrary) |
index.filter |
Indexes for variables that will be use for analysis in data vector |
n |
The size of the sample |
proportion |
The proportion of lowest P (Chi2) to be used when estimating the inflation factor Lambda for "regress" method only |
plot |
If TRUE, plot of lambda will be produced |
type_of_plot |
For developers only |
lmax |
The threshold for lambda for plotting (optional) |
color |
The color of the plot |
F |
The estimation of F (optional) |
K |
The estimation of K (optional) |
ladd |
The estimation of lambda for additive model (optional) |
clust |
For developers only |
vart0 |
For developers only |
tmp |
For developers only |
CA |
For developers only |
p.table |
For developers only |
A list with elements
Zx |
output vector corrected Chi square statistic |
vv |
output vector of VIF |
exeps |
output vector of exepsons (NA) |
calrate |
output vector of calrate |
F |
F |
K |
K |
Yakov Tsepilov
require(GenABEL.data) data(ge03d2) # truncate the data to make the example faster ge03d2 <- ge03d2[seq(from=1,to=nids(ge03d2),by=2),seq(from=1,to=nsnps(ge03d2),by=3)] qts <- mlreg(dm2~sex,data=ge03d2,gtmode = "dominant") chi2.1df <- results(qts)$chi2.1df s <- summary(ge03d2) freq <- s$Q.2 result <- VIFGC(p=freq,x=1,method = "median",CA=FALSE,data=chi2.1df,n=nids(ge03d2))