You could put the \input in a node and draw a rectangle relative to the corners of the node.

\begin{filecontents*}{table.tex}
\begin{tabular}{l*{3}{c}}
& A & B & C \\
\hline
1 & blah & blah & blah \\
2 & blah & blah & blah \\
3 & blah & blah & blah \\
\hline
\end{tabular}
\end{filecontents*}
\documentclass{beamer}
\usepackage{tikz}
\usetikzlibrary{calc}
\begin{document}
\begin{frame}
\begin{center}
\begin{tikzpicture}
\node (table) {\input{table.tex}};
\draw [red,ultra thick,rounded corners]
($(table.south west) !.3! (table.north west)$)
rectangle
($(table.south east) !.5! (table.north east)$);
\end{tikzpicture}
\end{center}
\end{frame}
\end{document}
Some explanation to the above code
There are several standard anchors on a node by default, denoted by compass directions, accessed with the syntax <node name>.<anchor>. For example will MyNode.north west be the top left corner of MyNode.
To get a coordinate between two existing coordinates you can use the TikZ library calc. This is described in section 13.5 Coordinate Calculations of the manual. It provides the syntax
($(<nodename or coordinate>) ! <factor> ! (<nodename or coordinate>)$)
Dollar signs indicate that a coordinate calculation should be done. The <factor> is a number saying how far, on the line between the two specified nodes, relative to the distance between the nodes, the point should be. For example,
($(0,0) !.3! (1,0)$)
is 30% of the way between (0,0) and (1,0), meaning (0.3,0).
In other words,
\draw [red,ultra thick,rounded corners]
($(table.south west) !.3! (table.north west)$)
rectangle
($(table.south east) !.5! (table.north east)$);
draws a rectangle from the point that is 30% of the distance from the lower left corner to the upper left corner, to the point that is halfway between the lower right and upper right corners.
blah, you output\somecode{stuff>}blah? – Werner Apr 16 '12 at 15:41table.texand add the code. However, because the statistical process is rerun over and over again, I would like to avoid that if possible. I don't expect the spacing of the table to change much, e.g. there will always be 4 digit numbers in the cells, albeit different digits. So, if a rectangle is overlaid at the right coordinates once, I wouldn't have to change the code much thereafter, if that makes any sense. – stanford202 Apr 16 '12 at 15:46pgfplotstableto typeset the table and add highlighting using the row number, or a keyword/key value. – Jake Apr 16 '12 at 16:35