# R/common-methods.R In izhbannikov/vartools: Variant Association Tools R-package

#### Defines functions check_argsgetUVsum_method

```sum_method <- function(U, V) {
# score statistic and p-value
if (abs(sum(U)) < 1e-20) {
score = 0
pval = 1
} else {
ones = rep(1, length(U))
score = sum(U) / sqrt(sum(V))
pval = 1 - pchisq(score^2, 1)
}
res = c(score, pval)
res
}

getUV <- function(y, X) {
# Internal function for getUV
# center phenotype y
y.new = y - mean(y)
# get score vector
U = colSums(y.new * X, na.rm=TRUE)

# get covariance matrix
X.new = scale(X, scale=FALSE)
if (sum(complete.cases(X)) != length(y))  { # missing data
tX.new = t(X.new)
Sx = matrix(0, ncol(X), ncol(X))
for (i in 1:nrow(tX.new))
{
for (j in i:ncol(X.new))
{
Sx[i,j] = sum(tX.new[i,] * X.new[,j], na.rm=TRUE)
}
}
sx.diag = diag(Sx)
Sx = Sx + t(Sx)
diag(Sx) = sx.diag
V = mean(y) * (1 - mean(y)) * Sx
} else {  # no missing data
V = mean(y) * (1 - mean(y)) * (t(X.new) %*% X.new)
}
# results
res.uv = list(U=U, V=V)
return(res.uv)
}

check_args <- function(y, X, perm) {
## Internal function to check argument:s y, X, perm

# y as numeric vector
if (!is.vector(y) || mode(y) != "numeric")
stop("Sorry, argument 'y' must be a numeric vector")
# no misssing values in y
if (any(is.na(y)))
stop("No missing data allowed in argument 'y' ")
# binary values (0, 1) in y
if (!all(y %in% c(0, 1)))
stop("Argument 'y' must contain only 0 and 1")
# X as matrix or data frame
if(!is.matrix(X) & !is.data.frame(X))
stop("Argument 'X' must be a matrix or data.frame")
# compatibility between X and y
if (nrow(X) != length(y))
stop("'X' and 'y' have different lengths")
# force X as matrix
if (!is.matrix(X)) X = as.matrix(X)
# permutations
if (mode(perm) != "numeric" || length(perm) != 1
|| perm < 0 || (perm %% 1) !=0)
{
warning("argument 'perm' incorrectly defined. Value perm=100 is used")
perm = 100
}
# results
list(y=y, X=X, perm=perm)
}
```
izhbannikov/vartools documentation built on May 17, 2017, 5:29 a.m.