Here is an example
tab1 = data.frame(x = c('a', 'b'), y = c('<a href="#b">New</a>'))
print(xtable(tab1), type = 'html', sanitize.text.function = function(x) x)
Note that you must be careful with the sanitize.text.function, since the default html escapes everything, whereas the identity function is used to prevent escaping of the hyperlinks.