From c5fedc9e623bc86d06e97ad1492af56180169860 Mon Sep 17 00:00:00 2001 From: Tremmel Date: Mon, 28 Jun 2021 16:37:12 +0200 Subject: [PATCH] add help --- R/fast_locusplot.R | 3 +++ man/fast_locusplot.Rd | 8 ++++---- 2 files changed, 7 insertions(+), 4 deletions(-) diff --git a/R/fast_locusplot.R b/R/fast_locusplot.R index 08fdaff..5820e87 100644 --- a/R/fast_locusplot.R +++ b/R/fast_locusplot.R @@ -4,6 +4,9 @@ #' @param build Genomic build. Currently only hg19 is supported. #' @param snp Default: top snp with lowest pvalue is taken. Otherwise specify any rsid id included in data. #' @param pop a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU". +#' @param show_MAF Show minor allele frequencies from specified 1000 Genomes population. Default = FALSE. +#' @param show_regulom Show RegulomeDB ranks. More information at https://regulomedb.org/regulome-help. Default = FALSE. +#' @param RDB_ranks Specify RegulomeDB ranks to show. Defaults are the most significants: 1 and 2 including subtypes a-f. #' @param color color scheme for R^2 values. Possible values are c("viridis","magma","inferno","plasma"). #' @param token !!!REQUIRED!!!: Register for token at https://ldlink.nci.nih.gov/?tab=apiaccess #' @return A ggplot2 object/plot diff --git a/man/fast_locusplot.Rd b/man/fast_locusplot.Rd index 57381e2..c4a2459 100644 --- a/man/fast_locusplot.Rd +++ b/man/fast_locusplot.Rd @@ -11,7 +11,7 @@ fast_locusplot( pop = "CEU", show_MAF = FALSE, show_regulom = FALSE, - RDB_ranks = c("1", "2"), + RDB_ranks = c(1, 2), color = "viridis", token = NULL ) @@ -25,11 +25,11 @@ fast_locusplot( \item{pop}{a 1000 Genomes Project population, (e.g. YRI or CEU), multiple allowed, default = "CEU".} -\item{show_MAF}{Show minor allele frequencies (MAF) using different sizes of points. Default=FALSE.} +\item{show_MAF}{Show minor allele frequencies from specified 1000 Genomes population. Default = FALSE.} -\item{show_regulom}{Show most significant RegulomeDB ranks. More information at https://regulomedb.org/regulome-help/. Default=FALSE.} +\item{show_regulom}{Show RegulomeDB ranks. More information at https://regulomedb.org/regulome-help. Default = FALSE.} -\item{RDB_ranks}{Specify ranks to show. Default= 1 and 2 including subtypes a-f.} +\item{RDB_ranks}{Specify RegulomeDB ranks to show. Defaults are the most significants: 1 and 2 including subtypes a-f.} \item{color}{color scheme for R^2 values. Possible values are c("viridis","magma","inferno","plasma").}