add tab_stuart.Rd

stuart/.Rhistory

@@ -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()

stuart/R/annot_giga-data.R

-#' 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"

stuart/R/annot_mega-data.R

-#' 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"

stuart/R/annot_mini-data.R

-#' 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"

stuart/R/annot_muga-data.R

-#' 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"

stuart/man/annot_giga.Rd

-% 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}

stuart/man/annot_mega.Rd

-% 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}

stuart/man/annot_mini.Rd

-% 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}

stuart/man/annot_muga.Rd

-% 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}

stuart/man/stuart_tab.Rd

+% 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}