fix issue #105 - document bf params as relating to log BF and not BF

R/susie.R

@@ -117,7 +117,7 @@ finemap.susie=function(dataset1, susie.args=list(),  ...) {
 ##'
 ##' @title run coloc using susie to detect separate signals
 ##' @inheritParams coloc.signals
-##' @param bf2 named vector of BF, names are snp ids and will be matched to column names of susie object's alpha
+##' @param bf2 named vector of log BF, names are snp ids and will be matched to column names of susie object's alpha
 ##' @param susie.args named list of arguments to be passed to susieR::susie_rss()
 ##' @param ... other arguments passed to \link{coloc.bf_bf}, in particular prior
 ##'   values for causal association with one trait (p1, p2) or both (p12)
@@ -148,7 +148,7 @@ coloc.susie_bf=function(dataset1,bf2, p1=1e-4, p2=1e-4, p12=5e-6, susie.args=lis
 ##'
 ##' @title Finemap data through Bayes factors
 ##' @inheritParams finemap.abf
-##' @param bf1 named vector of BF, or matrix of BF with colnames (cols=snps, rows=signals)
+##' @param bf1 named vector of log BF, or matrix of log BF with colnames (cols=snps, rows=signals)
 ##' @return finemap.signals style result
 ##' @export
 ##' @author Chris Wallace
@@ -211,8 +211,8 @@ finemap.bf=function(bf1, p1=1e-4) {
 ##'
 ##' @title Coloc data through Bayes factors
 ##' @inheritParams coloc.signals
-##' @param bf1 named vector of BF, or matrix of BF with colnames (cols=snps, rows=signals)
-##' @param bf2 named vector of BF, or matrix of BF with colnames (cols=snps, rows=signals)
+##' @param bf1 named vector of log BF, or matrix of BF with colnames (cols=snps, rows=signals)
+##' @param bf2 named vector of log BF, or matrix of BF with colnames (cols=snps, rows=signals)
 ##' @param trim_by_posterior it is important that the signals to be colocalised
 ##'   are covered by adequate numbers of snps in both datasets. If TRUE, signals
 ##'   for which snps in common do not capture least overlap.min proportion of