[GenABEL-dev] [Genabel-commits] r688 - pkg/GenABEL/R

[Yurii Aulchenko]

As promised, updated polygenic_hglm parameters + did the documentation
cross-linking

Yurii

On Tue, Mar 8, 2011 at 12:26 AM,  <noreply at r-forge.wu-wien.ac.at> wrote:
> Author: yurii
> Date: 2011-03-08 00:26:01 +0100 (Tue, 08 Mar 2011)
> New Revision: 688
>
> Modified:
>   pkg/GenABEL/R/GenABEL-package.R
>   pkg/GenABEL/R/polygenic.R
>   pkg/GenABEL/R/polygenic_hglm.R
> Log:
> update on polygenic_hglm parameters + documentation cross-linking
>
> Modified: pkg/GenABEL/R/GenABEL-package.R
> ===================================================================
> --- pkg/GenABEL/R/GenABEL-package.R     2011-03-07 23:24:59 UTC (rev 687)
> +++ pkg/GenABEL/R/GenABEL-package.R     2011-03-07 23:26:01 UTC (rev 688)
> @@ -104,6 +104,7 @@
>  #' \code{\link{ibs}} (computations of IBS / genomic IBD),
>  #' \code{\link{egscore}} (stratification adjustment following Price et al.),
>  #' \code{\link{polygenic}} (heritability analysis),
> +#' \code{\link{polygenic_hglm}} (another function for heritability analysis),
>  #' \code{\link{mmscore}} (score test of Chen and Abecasis),
>  #' \code{\link{grammar}} (grammar test of Aulchenko et al.).
>  #'
>
> Modified: pkg/GenABEL/R/polygenic.R
> ===================================================================
> --- pkg/GenABEL/R/polygenic.R   2011-03-07 23:24:59 UTC (rev 687)
> +++ pkg/GenABEL/R/polygenic.R   2011-03-07 23:26:01 UTC (rev 688)
> @@ -129,7 +129,12 @@
>  #' If a trait (no covarites) is used, make sure that order of IDs in
>  #' kinship.matrix is exactly the same as in the outcome
>  #'
> +#' Please note that there is alternative to 'polygenic',
> +#' \code{\link{polygenic_hglm}}, which is faster than
> +#' 'polygenic'.
> +#'
>  #' @seealso
> +#' \code{\link{polygenic_hglm}},
>  #' \code{\link{mmscore}},
>  #' \code{\link{grammar}}
>  #'
>
> Modified: pkg/GenABEL/R/polygenic_hglm.R
> ===================================================================
> --- pkg/GenABEL/R/polygenic_hglm.R      2011-03-07 23:24:59 UTC (rev 687)
> +++ pkg/GenABEL/R/polygenic_hglm.R      2011-03-07 23:26:01 UTC (rev 688)
> @@ -2,6 +2,8 @@
>  #'
>  #' Estimation of polygenic model using hierarchical
>  #' GLM (hglm package)
> +#' Tell when REML is used, what otherwise;
> +#' what it is doing, how to do tests, add more examples, references, etc.
>  #'
>  #' @param formula Formula describing fixed effects to be used in analysis, e.g.
>  #' y ~ a + b means that outcome (y) depends on two covariates, a and b.
> @@ -14,6 +16,8 @@
>  #' @param family a description of the error distribution and link function to be
>  #' used in the mean part of the model (see \code{\link{family}} for details of
>  #' family functions)
> +#' @param conv 'conv' parameter of 'hglm' (stricter then default)
> +#' @param maxit 'maxit' parameter of 'hglm' (stricter then default)
>  #' @param ... other parameters passed to 'hglm' call
>  #'
>  #' @author Xia Shen, Yurii Aulchenko
> @@ -22,9 +26,9 @@
>  #' need to put reference here
>  #'
>  #' @seealso
> +#' \code{\link{polygenic}},
>  #' \code{\link{mmscore}},
>  #' \code{\link{grammar}}
> -#' \code{\link{polygenic}}
>  #'
>  #' @examples
>  #' data(ge03d2ex.clean)
> @@ -46,7 +50,7 @@
>  #'
>  #' @keywords htest
>  #'
> -"polygenic_hglm" <- function(formula,kinship.matrix,data,family=gaussian(), ... )
> +"polygenic_hglm" <- function(formula,kinship.matrix,data,family=gaussian(), conv=1e-8, maxit=100, ... )
>  {
>        if (!require(hglm))
>                stop("this function requires 'hglm' package to be installed")
> @@ -71,7 +75,9 @@
>        relmat <- relmat*2.0
>        s <- svd(relmat)
>        L <- s$u %*% diag(sqrt(s$d))
> -       res_hglm <- hglm(y = y, X = desmat, Z = L, family = family, ... )
> +       cnv <- 1e-6
> +       mxit <- 40
> +       res_hglm <- hglm(y = y, X = desmat, Z = L, family = family, conv = conv, maxit = maxit, ... )
>        #sum_res_hglm <- summary(res_hglm)
>
>        out <- list()
>
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