diff --git a/DESCRIPTION b/DESCRIPTION index 2d535bf..8922184 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: polyRAD Version: 0.1 -Date: 2019-01-02 +Date: 2019-01-09 Title: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids Authors@R: c(person("Lindsay V.", "Clark", email = "lvclark@illinois.edu", role = c("aut", "cre")), diff --git a/README.md b/README.md index 06f0f2a..3eb6a73 100644 --- a/README.md +++ b/README.md @@ -34,6 +34,10 @@ install.packages("polyRAD_0.x.zip", repos = NULL) replacing the file name with the one you just downloaded. +## Tutorial + +The tutorial document for the package is available [on Github](https://github.com/lvclark/polyRAD/raw/master/vignettes/polyRADtutorial.pdf). + ## Funding This material is based upon work supported by the National Science Foundation under Grant No. diff --git a/vignettes/polyRADtutorial.Rnw b/vignettes/polyRADtutorial.Rnw index c1767c4..5b13f86 100644 --- a/vignettes/polyRADtutorial.Rnw +++ b/vignettes/polyRADtutorial.Rnw @@ -32,6 +32,46 @@ A single ``RADdata'' object contains the entire dataset of read depth and locus information, as well as parameters that are estimated during the course of analysis. +\section{Summary of available functions} + +For any function named in this section, see its help page for more information. +(For example by typing \texttt{?VCF2RADdata} into the R console.) + +Several functions are available for import of read depth data and (optionally) +alignment information into a RADdata object: + +\begin{itemize} +\item \texttt{VCF2RADdata} +\item \texttt{readTagDigger} +\item \texttt{readStacks1} +\item \texttt{readHMC} +\end{itemize} + +More generally, the \texttt{RADdata} function is used for constructing RADdata +objects; see the help page for that function for more information on what +data are needed. + +Several pipelines are available for genotype estimation, depending on how the +population is structured (i.e. what the genotype prior probabilities should be.): + +\begin{itemize} +\item \texttt{PipelineMapping2Parents} +\item \texttt{IterateHWE} +\item \texttt{IteratePopStruct} +\end{itemize} + +Lastly, for exporting the estimated genotypes to other software: + +\begin{itemize} +\item \texttt{ExportGAPIT} +\item \texttt{Export\_rrBLUP\_Amat} +\item \texttt{Export\_rrBLUP\_GWAS} +\end{itemize} + +If you need continuous numerical genotypes exported in some other format, see +\texttt{GetWeightedMeanGenotypes}. Also, \texttt{GetLikelyGen} returns the +most likely genotypes for a single sample. + \section{Estimating genotype probabilities in a mapping population} In this example, we'll import some data from an F1 mapping population diff --git a/vignettes/polyRADtutorial.pdf b/vignettes/polyRADtutorial.pdf index ffee53d..002d38b 100644 Binary files a/vignettes/polyRADtutorial.pdf and b/vignettes/polyRADtutorial.pdf differ