Commit 82a1b397 authored by Marie Bourdon's avatar Marie Bourdon
Browse files

add tab_stuart.Rd

parent a85c45ed
......@@ -146,3 +146,11 @@ strains <- geno_strains(ref=annot_mini,geno=genos,par1=c("StrainsA_1","StrainsA_
head(strains)
genos <- genos %>% filter(!Sample.ID %in% c("StrainsA_1", "StrainsA_2", "StrainsB_1","StrainsB_2"))
data(stuart_tab)
devtools::build(vignettes=TRUE)
devtools::install(build_vignettes=TRUE)
browseVignettes(stuart)
browseVignettes("stuart")
use_readme_rmd()
usethis::use_readme_rmd()
build_readme()
devtools::build_readme()
#' Data frame with gigaMUGA markers annotation
#'
#' A dataset containing gigaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
#'
#' @format A data frame with 143259 rows and 8 variables
#' \describe{
#' \item{marker}{name of the marker}
#' \item{chr}{chromosome}
#' \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
#' \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
#' \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
#' \item{snp}{marker alleles}
#' \item{unique}{indicates if the marker maps uniquely on mm10}
#' \item{unmapped}{indicates if the marker does not map perfectly on mm10}
#' }
"annot_giga"
#' Data frame with megaMUGA markers annotation
#'
#' A dataset containing megaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
#'
#' @format A data frame with 77808 rows and 8 variables
#' \describe{
#' \item{marker}{name of the marker}
#' \item{chr}{chromosome}
#' \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
#' \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
#' \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
#' \item{snp}{marker alleles}
#' \item{unique}{indicates if the marker maps uniquely on mm10}
#' \item{unmapped}{indicates if the marker does not map perfectly on mm10}
#' }
"annot_mega"
#' Data frame with miniMUGA markers annotation
#'
#' A dataset containing miniMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/mini_revisited.html).
#'
#' @format A data frame with 11125 rows and 8 variables
#' \describe{
#' \item{marker}{name of the marker}
#' \item{chr}{chromosome}
#' \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
#' \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
#' \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
#' \item{snp}{marker alleles}
#' \item{unique}{indicates if the marker maps uniquely on mm10}
#' \item{unmapped}{indicates if the marker does not map perfectly on mm10}
#' }
"annot_mini"
#' Data frame with MUGA markers annotation
#'
#' A dataset containing MUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/muga_annotations.html).
#'
#' @format A data frame with 7854 rows and 8 variables
#' \describe{
#' \item{marker}{name of the marker}
#' \item{chr}{chromosome}
#' \item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
#' \item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
#' \item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
#' \item{snp}{marker alleles}
#' \item{unique}{indicates if the marker maps uniquely on mm10}
#' \item{unmapped}{indicates if the marker does not map perfectly on mm10}
#' }
"annot_muga"
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/annot_giga-data.R
\docType{data}
\name{annot_giga}
\alias{annot_giga}
\title{Data frame with gigaMUGA markers annotation}
\format{
A data frame with 143259 rows and 8 variables
\describe{
\item{marker}{name of the marker}
\item{chr}{chromosome}
\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
\item{snp}{marker alleles}
\item{unique}{indicates if the marker maps uniquely on mm10}
\item{unmapped}{indicates if the marker does not map perfectly on mm10}
}
}
\usage{
annot_giga
}
\description{
A dataset containing gigaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
}
\keyword{datasets}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/annot_mega-data.R
\docType{data}
\name{annot_mega}
\alias{annot_mega}
\title{Data frame with megaMUGA markers annotation}
\format{
A data frame with 77808 rows and 8 variables
\describe{
\item{marker}{name of the marker}
\item{chr}{chromosome}
\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
\item{snp}{marker alleles}
\item{unique}{indicates if the marker maps uniquely on mm10}
\item{unmapped}{indicates if the marker does not map perfectly on mm10}
}
}
\usage{
annot_mega
}
\description{
A dataset containing megaMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/new_annotations.html).
}
\keyword{datasets}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/annot_mini-data.R
\docType{data}
\name{annot_mini}
\alias{annot_mini}
\title{Data frame with miniMUGA markers annotation}
\format{
A data frame with 11125 rows and 8 variables
\describe{
\item{marker}{name of the marker}
\item{chr}{chromosome}
\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
\item{snp}{marker alleles}
\item{unique}{indicates if the marker maps uniquely on mm10}
\item{unmapped}{indicates if the marker does not map perfectly on mm10}
}
}
\usage{
annot_mini
}
\description{
A dataset containing miniMUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/mini_revisited.html).
}
\keyword{datasets}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/annot_muga-data.R
\docType{data}
\name{annot_muga}
\alias{annot_muga}
\title{Data frame with MUGA markers annotation}
\format{
A data frame with 7854 rows and 8 variables
\describe{
\item{marker}{name of the marker}
\item{chr}{chromosome}
\item{bp_mm10}{localisation on chromosome in bp (mm10 assembly)}
\item{cM_cox}{localisation on chromosome in cM (from Cox et al.)}
\item{cM_g2f1}{localisation on chromosome in cM (from Liu et al.)}
\item{snp}{marker alleles}
\item{unique}{indicates if the marker maps uniquely on mm10}
\item{unmapped}{indicates if the marker does not map perfectly on mm10}
}
}
\usage{
annot_muga
}
\description{
A dataset containing MUGA markers positions and other information from by Karl Broman (https://kbroman.org/MUGAarrays/muga_annotations.html).
}
\keyword{datasets}
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/stuart_tab-data.R
\docType{data}
\name{stuart_tab}
\alias{stuart_tab}
\title{Output of tab_mark function}
\format{
A data frame with 11125 rows and 7 variables
\describe{
\item{SNP.Name}{name of the marker}
\item{Allele_1}{first allele of the marker}
\item{Allele_2}{second allele of the marker}
\item{n_HM1}{number of homozygous individuals for the first allele}
\item{n_HM2}{number of homozygous individuals for the second allele}
\item{n_HT}{number of heterozygous individuals}
\item{n_NA}{number of non genotyped individuals}
}
}
\usage{
stuart_tab
}
\description{
A dataset with the output of tab_mark() function.
}
\keyword{datasets}
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