Sec-DataTypes2.Rnw

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<<knitr, echo=FALSE>>=
opts_chunk$set(tidy.opts = 
               list(width.cutoff = 50, 
                    tidy = FALSE),
               fig.align = 'center',
               stop_on_error = 1L,
               comment = NA,
               prompt = TRUE)
options(width = 60)
@ 

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\subsection*{Matrices}

\begin{frame}[fragile]
  \begin{block}{Matrices are 2-dimensional vectors}
<<mat>>=
m <- matrix(1:12, nrow = 4, ncol = 3)
m
dim(m)
ncol(m) ## and also nrow(m)
@
\end{block}
\end{frame}

\begin{frame}[fragile]
What if I don't get the data or dimensions right?
<<mat2>>=
matrix(1:11, 4, 3)
matrix(1:12, 3, 3)
@   
\end{frame}


%% \begin{frame}[fragile]
%% <<mat3>>=
%% x <- 1:12
%% dim(x)
%% dim(x) <- c(4, 3)
%% x
%% class(x)
%% @     
%% \end{frame}

\begin{frame}[fragile]
  \begin{block}{Subsetting matrices}
<<submat>>=
dim(m)
m[3:4, 2:3]
m[1, ]
m[, 1]
@     
  \end{block}  
\end{frame}

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\subsection*{Arrays}

\begin{frame}[fragile]
  \begin{block}{Arrays are n-dimensional vectors}
<<arrays>>=
array(1:16, dim = c(2, 4, 2))
@     
  \end{block}  
\end{frame}

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\subsection*{Lists}

\begin{frame}[fragile]
  \begin{block}{Lists are ordered set of arbitrary \R objects.}
<<list>>=
ll <- list(a = 1:3, b = letters[1:2])
ll
ll[[1]]
ll$b
@     
\end{block}
\end{frame}

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\subsection*{Data frames}

\begin{frame}[fragile]
  \begin{block}{Dataframes are 2-dimensional list.}  
<<dfr, tidy = FALSE>>=
dfr <- data.frame(type = c("A", "A", "B", "B"),
                  time = rnorm(4))
dfr
@ 
\end{block}
\end{frame}

\begin{frame}[fragile]
<<dfr2>>=
dfr[1,]
dfr[1, "time"]
dfr$time
@ 
\end{frame}

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%% \subsection*{Evironments}

%% \begin{frame}[fragile]
%%   \begin{block}{An environment is an unordered collection of objects}
%% <<env>>=
%% e <- new.env()
%% e[["a"]] <- 1:3
%% assign("b", "CSAMA", envir = e)
%% ls(e)
%% e$a
%% get("b", e)
%% @ 
%%   \end{block}
%% \end{frame}

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\subsection*{Names}

\begin{frame}[fragile]
  \begin{block}{Names}
    We have seen that function arguments have names, and named our \Robject{data.frame} columns. We can also name \Robject{matrix}/\Robject{data.frame} columns and rows, dimensions, and vector items.
  \end{block}
<<names>>=
x <- c(a = 1, b = 2)
x
names(x)
@   
\end{frame}

\begin{frame}[fragile]
<<matdimnames0, tidy = FALSE>>=
M <- matrix(c(4, 8, 5, 6, 4, 2, 1, 5, 7), nrow=3)
colnames(M) <- c(2005, 2006, 2007)
rownames(M) <- c("plane", "bus", "boat")
M
M[c("plane", "boat"), "2005"]
@ 
\end{frame}

\begin{frame}[fragile]
<<matdimnames, tidy = FALSE>>=
M <- matrix(c(4, 8, 5, 6, 4, 2, 1, 5, 7), nrow=3)
dimnames(M) <- list(year = 
                    c(2005, 2006, 2007),
                    "mode of transport" =                     
                    c("plane", "bus", "boat"))
M
@ 
\end{frame}


\begin{frame}[fragile]
  \begin{block}{Subsetting with numbers, characters, logicals}
<<subsetsmry>>=
x <- 1:5
names(x) <- letters[1:5]
x[c(1, 3)]
x[c("a", "c")]
x[c(TRUE, FALSE, TRUE, FALSE, FALSE)]
@ 

    
  \end{block}  
\end{frame}

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\subsection*{Factors}

\begin{frame}[fragile]
  \begin{block}{Factors represent categorical data}
<<fac>>=
gender_char <- sample(c("M", "F"), 10, replace = TRUE)
gender_fac <- factor(gender_char)
gender_fac
@     
  \end{block}
\end{frame}



\begin{frame}[fragile]
  \begin{block}{Special values}
<<specialvals, eval=FALSE>>=
NULL; is.null()
NA; NaN; is.na()
Inf; -Inf; is.infinite()
@     
  \end{block}
\begin{block}{}
  What are the mode and types of these?
\end{block}
\end{frame}


\subsection{Exercise}

\begin{frame}{\exercise}
  \begin{block}{How to store microarray data?}
    \begin{itemize}
    \item What information do we want to store?
    \item How to store these individual pieces of information?
    \item How to store these together?
    \end{itemize}    
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \begin{block}{The \Rfunction{paste} function}
<<paste>>=
paste("A", "B", "C", sep = "-")
paste0("A", "B", "C") ## sep = ""
@         
  \end{block}
  \begin{block}{Normally distributed data}
<<rnorm>>=
rnorm(3)
rnorm(5, mean = 10, sd = 2)
@     
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \begin{block}{The expression data}
<<maex0, tidy = FALSE>>=
expdata <- matrix(rnorm(200), nrow = 50, ncol = 4)
dimnames(expdata) <- 
  list(features = paste0("gene", 1:nrow(expdata)),
       samples = paste0("sample", 1:ncol(expdata)))
head(expdata)
@   
See \texttt{Exercise-03.R}


\end{block}
\end{frame}

\begin{frame}[fragile]
  \begin{block}{Sample description}
<<maex1, tidy = FALSE>>=
smdata <- data.frame(feature = colnames(expdata),
                     group = c("ctrl", "ctrl",
                       "cond1", "cond1"),
                     replicate = rep(1:2, each = 2))
smdata
@   
See \texttt{Exercise-03.R}
\end{block}
\end{frame}

\begin{frame}[fragile]
  \begin{block}{Feature description}    
<<maex2, tidy = FALSE, eval = FALSE>>=
fmdata <- data.frame(feature = rownames(expdata),
                     description = ...)
@   
See \texttt{Exercise-03.R}
  \end{block}
\end{frame}

\begin{frame}[fragile]
  \begin{block}{The complete experiment}   
<<maex3, tidy = FALSE, eval = FALSE>>=
marray <- list(
  expression = expdata,
  featuremeta = fmdata,
  samplemeta = smdata)
@   
See \texttt{Exercise-03.R}
  \end{block}
\end{frame}