From ce712413e8db476dbde215c16e2eed486a5874d8 Mon Sep 17 00:00:00 2001 From: Gibran Hemani Date: Mon, 12 Oct 2020 13:34:59 +0100 Subject: [PATCH] updated documentation --- DESCRIPTION | 2 +- R/harmonise.R | 6 +++--- man/harmonise_data.Rd | 6 +++--- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index b5cf4e85..12612dab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -59,7 +59,7 @@ Remotes: License: MIT + file LICENSE LazyData: true VignetteBuilder: knitr -RoxygenNote: 7.1.0 +RoxygenNote: 7.1.1 Encoding: UTF-8 Suggests: covr, diff --git a/R/harmonise.R b/R/harmonise.R index e57029a5..2739e77a 100644 --- a/R/harmonise.R +++ b/R/harmonise.R @@ -36,9 +36,9 @@ #' @param exposure_dat Output from \code{read_exposure_data}. #' @param outcome_dat Output from \code{extract_outcome_data}. #' @param action Level of strictness in dealing with SNPs. -#' * `action = 1`: Assume all reference alleles are on the positive strand, i.e. do nothing (warning - this is very risky and is not recommended); -#' * `action = 2`: Try to infer positive strand alleles, using allele frequencies for palindromes; -#' * `action = 3`: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis. +#' * `action = 1`: Assume all alleles are coded on the forward strand, i.e. do not attempt to flip alleles +#' * `action = 2`: Try to infer positive strand alleles, using allele frequencies for palindromes (default, conservative); +#' * `action = 3`: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis (more conservative). #' If a single value is passed then this action is applied to all outcomes. #' But multiple values can be supplied as a vector, each element relating to a different outcome. #' diff --git a/man/harmonise_data.Rd b/man/harmonise_data.Rd index d13b3161..30e32b31 100644 --- a/man/harmonise_data.Rd +++ b/man/harmonise_data.Rd @@ -13,9 +13,9 @@ harmonise_data(exposure_dat, outcome_dat, action = 2) \item{action}{Level of strictness in dealing with SNPs. \itemize{ -\item \code{action = 1}: Assume all reference alleles are on the positive strand, i.e. do nothing (warning - this is very risky and is not recommended); -\item \code{action = 2}: Try to infer positive strand alleles, using allele frequencies for palindromes; -\item \code{action = 3}: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis. +\item \code{action = 1}: Assume all alleles are coded on the forward strand, i.e. do not attempt to flip alleles +\item \code{action = 2}: Try to infer positive strand alleles, using allele frequencies for palindromes (default, conservative); +\item \code{action = 3}: Correct strand for non-palindromic SNPs, and drop all palindromic SNPs from the analysis (more conservative). If a single value is passed then this action is applied to all outcomes. But multiple values can be supplied as a vector, each element relating to a different outcome. }}