48 lines
1.4 KiB
R
48 lines
1.4 KiB
R
% Generated by roxygen2: do not edit by hand
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% Please edit documentation in R/mash-evaluation.R
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\name{mash_plot_manhattan_by_condition}
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\alias{mash_plot_manhattan_by_condition}
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\title{Manhattan plot in ggplot colored by significant conditions}
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\usage{
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mash_plot_manhattan_by_condition(
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m,
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snp,
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cond = NA,
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saveoutput = FALSE,
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suffix = "",
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thresh = 0.05
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)
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}
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\arguments{
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\item{m}{A mash object (outputted by mash).}
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\item{snp}{A bigSNP object, produced by the bigsnpr package. Here,
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the WAMI SNP information.}
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\item{cond}{A vector of phenotypes. Defaults to the names of each
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column in the mash object.}
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\item{saveoutput}{Logical. Should the output be saved to the path?}
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\item{suffix}{Character. Optional. A unique suffix used to save the files,
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instead of the current date & time.}
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\item{thresh}{Numeric. The threshold used for the local false sign rate to
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call significance in a condition.}
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}
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\value{
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A \code{tbl_df()} of the data used to make the Manhattan plot, and a
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ggplot object containing the Manhattan.
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}
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\description{
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Takes a mash object and, for some vector of phenotypes, returns
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a Manhattan plot ggplot object (and its dataframe). Each SNP in the plot
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is colored by the number of phenotypes it is significant for. Even and
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odd chromosomes have different shapes for their SNPs, so that
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chromosome identity can be determined.
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}
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\examples{
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\dontrun{manhattan_out <- mash_ggman_by_condition(m = m, saveoutput = TRUE)}
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}
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