From bb995ecb6fbda88915081df8371482b0e7d65849 Mon Sep 17 00:00:00 2001 From: "L.C. Karssen" Date: Thu, 21 Mar 2024 11:44:51 +0000 Subject: [PATCH] Spelling fixes in the vignette --- vignettes/IntroToAnnotationPackages.Rnw | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/vignettes/IntroToAnnotationPackages.Rnw b/vignettes/IntroToAnnotationPackages.Rnw index 105567d..8ea16ec 100644 --- a/vignettes/IntroToAnnotationPackages.Rnw +++ b/vignettes/IntroToAnnotationPackages.Rnw @@ -82,10 +82,10 @@ they are described in this vignette. They can currently be used with all chip, organism, and \Rclass{TxDb} packages along with the popular GO.db package. -For the older less popular packages, there are still conventient ways +For the older less popular packages, there are still convenient ways to retrieve the data. The \emph{How to use bimaps from the ".db" annotation packages} vignette in the \Rpackage{AnnotationDbi} -package is a key reference for learnign about how to use bimap +package is a key reference for learning about how to use bimap objects. Finally, all of the `.db' (and most other \Bioconductor{} annotation @@ -100,7 +100,7 @@ As previously mentioned, a new set of methods have been added that allow a simpler way of extracting identifier based annotations. All the annotation packages that support these new methods expose an object named exactly the same as the package itself. These objects -are collectively called \Rclass{AnntoationDb} objects for the class +are collectively called \Rclass{AnnotationDb} objects for the class that they all inherit from. The more specific classes (the ones that you will actually see in the wild) have names like \Rclass{OrgDb}, \Rclass{ChipDb} or \Rclass{TxDb} objects. These names correspond to @@ -113,7 +113,7 @@ In addition, another accessor has recently been added which allows extraction of one column at at time. the \Rfunction{mapIds} method allows users to extract data into either a named character vector, a list or even a SimpleCharacterList. This method should work with all -the different kinds of \Rclass{AnntoationDb} objects described below. +the different kinds of \Rclass{AnnotationDb} objects described below. \section{ChipDb objects and the select method} @@ -146,7 +146,7 @@ We can look at this object to learn more about it: hgu95av2.db @ -If we want to know what kinds of data are retriveable via +If we want to know what kinds of data are retrievable via \Rfunction{select}, then we should use the \Rfunction{columns} method like this: @@ -163,7 +163,7 @@ mean. help("SYMBOL") @ -If we are curious about what kinds of fields we could potentiall use +If we are curious about what kinds of fields we could potentially use as keys to query the database, we can use the \Rfunction{keytypes} method. In a perfect world, this method will return values very similar to what was returned by \Rfunction{columns}, but in reality, @@ -259,7 +259,7 @@ select(org.Hs.eg.db, keys=uniKeys, columns=cols, keytype="UNIPROT") \end{Solution} So how could you use select to annotate your results? This next -exercise should hlep you to understand how that should generally work. +exercise should help you to understand how that should generally work. \begin{Exercise} Please run the following code snippet (which will load a fake data