From e6706b1abffa3a06ad09abb7b958e4f4375b598c Mon Sep 17 00:00:00 2001
From: Clare <chorscroft@users.noreply.github.com>
Date: Tue, 14 Jul 2020 14:38:23 +0100
Subject: [PATCH] Edited description of function and format of @seealso section
of documentation
---
R/create_LDprofile.R | 4 +++-
man/create_LDprofile.Rd | 4 +++-
2 files changed, 6 insertions(+), 2 deletions(-)
diff --git a/R/create_LDprofile.R b/R/create_LDprofile.R
index c89fc35..331bf49 100644
--- a/R/create_LDprofile.R
+++ b/R/create_LDprofile.R
@@ -10,6 +10,8 @@
#' If the \code{max_dist} is not an increment of \code{bin_size}, it will be adjusted to the next highest increment. The final bin will be the bin that \code{max_dist} falls into. For example, if the \code{max_dist} is given as 4.5 and the \code{bin_size} is 1, the final bin will be 4.\cr
#' By default, Beta parameters are not calculated. To fit a Beta distribution to the expected correlations, needed for the \code{\link{Zalpha_BetaCDF}} and \code{\link{Zbeta_BetaCDF}} statistics, \code{beta_params} should be set to TRUE and the package 'fitdistrplus' must be installed.
#'
+#' Ideally, an LD profile would be generated using data from a null population with no selection, For example by using a simulation if the other population parameters are known. However, often these are unknown or complex, so generating an LD profile using the same data as is being analysed is acceptable, as long as the bins are large enough.
+#'
#' @importFrom stats cor sd
#'
#' @param dist A numeric vector, or a list of numeric vectors, containing the genetic distance for each SNP.
@@ -32,7 +34,7 @@
#'
#'
#' @export
-#' @seealso \code{\link{Zalpha_expected}} \code{\link{Zalpha_rsq_over_expected}} \code{\link{Zalpha_log_rsq_over_expected}} \code{\link{Zalpha_Zscore}} \code{\link{Zalpha_BetaCDF}} \code{\link{Zbeta_expected}} \code{\link{Zbeta_rsq_over_expected}} \code{\link{Zbeta_log_rsq_over_expected}} \code{\link{Zbeta_Zscore}} \code{\link{Zbeta_BetaCDF}} \code{\link{Zalpha_all}}
+#' @seealso \code{\link{Zalpha_expected}}, \code{\link{Zalpha_rsq_over_expected}}, \code{\link{Zalpha_log_rsq_over_expected}}, \code{\link{Zalpha_Zscore}}, \code{\link{Zalpha_BetaCDF}}, \code{\link{Zbeta_expected}}, \code{\link{Zbeta_rsq_over_expected}}, \code{\link{Zbeta_log_rsq_over_expected}}, \code{\link{Zbeta_Zscore}}, \code{\link{Zbeta_BetaCDF}}, \code{\link{Zalpha_all}}.
#'
create_LDprofile<-function(dist,x,bin_size,max_dist=NULL,beta_params=FALSE){
diff --git a/man/create_LDprofile.Rd b/man/create_LDprofile.Rd
index 15e3d52..b5d70a4 100644
--- a/man/create_LDprofile.Rd
+++ b/man/create_LDprofile.Rd
@@ -30,6 +30,8 @@ Both lists should be the same length and should correspond exactly to each other
In the output, bins represent lower bounds. The first bin contains pairs where the genetic distance is greater than or equal to 0 and less than \code{bin_size}. The final bin contains pairs where the genetic distance is greater than or equal to \code{max_dist}-\code{bin_size} and less than \code{max_dist}.
If the \code{max_dist} is not an increment of \code{bin_size}, it will be adjusted to the next highest increment. The final bin will be the bin that \code{max_dist} falls into. For example, if the \code{max_dist} is given as 4.5 and the \code{bin_size} is 1, the final bin will be 4.\cr
By default, Beta parameters are not calculated. To fit a Beta distribution to the expected correlations, needed for the \code{\link{Zalpha_BetaCDF}} and \code{\link{Zbeta_BetaCDF}} statistics, \code{beta_params} should be set to TRUE and the package 'fitdistrplus' must be installed.
+
+Ideally, an LD profile would be generated using data from a null population with no selection, For example by using a simulation if the other population parameters are known. However, often these are unknown or complex, so generating an LD profile using the same data as is being analysed is acceptable, as long as the bins are large enough.
}
\examples{
## load the snps example dataset
@@ -47,5 +49,5 @@ if (requireNamespace("fitdistrplus", quietly = TRUE)==TRUE) {
Jacobs, G.S., T.J. Sluckin, and T. Kivisild, \emph{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps.} Genetics, 2016. \strong{203}(4): p. 1807
}
\seealso{
-\code{\link{Zalpha_expected}} \code{\link{Zalpha_rsq_over_expected}} \code{\link{Zalpha_log_rsq_over_expected}} \code{\link{Zalpha_Zscore}} \code{\link{Zalpha_BetaCDF}} \code{\link{Zbeta_expected}} \code{\link{Zbeta_rsq_over_expected}} \code{\link{Zbeta_log_rsq_over_expected}} \code{\link{Zbeta_Zscore}} \code{\link{Zbeta_BetaCDF}} \code{\link{Zalpha_all}}
+\code{\link{Zalpha_expected}}, \code{\link{Zalpha_rsq_over_expected}}, \code{\link{Zalpha_log_rsq_over_expected}}, \code{\link{Zalpha_Zscore}}, \code{\link{Zalpha_BetaCDF}}, \code{\link{Zbeta_expected}}, \code{\link{Zbeta_rsq_over_expected}}, \code{\link{Zbeta_log_rsq_over_expected}}, \code{\link{Zbeta_Zscore}}, \code{\link{Zbeta_BetaCDF}}, \code{\link{Zalpha_all}}.
}
--
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