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Spelling fixes in the vignette #13

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14 changes: 7 additions & 7 deletions vignettes/IntroToAnnotationPackages.Rnw
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Expand Up @@ -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
Expand All @@ -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
Expand All @@ -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}

Expand Down Expand Up @@ -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:

Expand All @@ -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,
Expand Down Expand Up @@ -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
Expand Down