How to see source code of a function/method in R?

If it's an internal function of R (e.g. from base package), just type the function name, like

> rowMeans

function (x, na.rm = FALSE, dims = 1L) 

{

    if (is.data.frame(x)) 

        x <- as.matrix(x)

    if (!is.array(x) || length(dn <- dim(x)) < 2L) 

        stop("'x' must be an array of at least two dimensions")

    if (dims < 1L || dims > length(dn) - 1L) 

        stop("invalid 'dims'")

    p <- prod(dn[-(1L:dims)])

    dn <- dn[1L:dims]

    z <- if (is.complex(x)) 

        .Internal(rowMeans(Re(x), prod(dn), p, na.rm)) + (0+1i) * 

            .Internal(rowMeans(Im(x), prod(dn), p, na.rm))

    else .Internal(rowMeans(x, prod(dn), p, na.rm))

    if (length(dn) > 1L) {

        dim(z) <- dn

        dimnames(z) <- dimnames(x)[1L:dims]

    }

    else names(z) <- dimnames(x)[[1L]]

    z

}

<bytecode: 0x111390028>

<environment: namespace:base>

If it's a S4 function in a package, e.g. to see the code of plotMA in the DESeq2 package, first find the object it belongs to using showMethods(), like

> showMethods('plotMA')

Function: plotMA (package BiocGenerics)

object="ANY"

object="character"

    (inherited from: object="ANY")

object="DESeqDataSet"

then to get source code by getMethod(), 

> getMethod("plotMA","DESeqDataSet")

Method Definition:

function (object, ...) 

{

    .local <- function (object, lfcColname, pvalues, pvalCutoff = 0.1, 

        ylim, linecol = "#ff000080", pointcol = c("black", "red"), 

        xlab, ylab, log = "x", cex = 0.45, ...) 

    {

        if (missing(xlab)) 

            xlab <- "mean of normalized counts"

        if (missing(ylab)) 

            ylab <- expression(log[2] ~ fold ~ change)

        if (!missing(pvalues)) {

            if (length(pvalues) != nrow(object)) {

                stop("length of pvalues should be equal to the number of rows of object")

            }

        }

        stopifnot(length(pointcol) == 2)

        if (!"results" %in% mcols(mcols(object))$type) {

            stop("first run DESeq() in order to produce an MA-plot")

        }

        if (missing(lfcColname)) {

            lfcColname <- lastCoefName(object)

        }

        if (length(lfcColname) != 1 | !is.character(lfcColname)) {

            stop("the argument 'lfcColname' should be a character vector of length 1")

        }

        if (missing(pvalues)) {

            res <- results(object, name = lfcColname)

            pvalues <- res$padj

        }

        x <- mcols(object)

        stopifnot(length(cex) == 1)

        col <- ifelse(is.na(pvalues) | pvalues > pvalCutoff, 

            pointcol[1], pointcol[2])

        col = col[x$baseMean > 0]

        x = x[x$baseMean > 0, ]

        py = x[, lfcColname]

        if (missing(ylim)) 

            ylim = c(-1, 1) * quantile(abs(py[is.finite(py)]), 

                probs = 0.99) * 1.1

        plot(x$baseMean, pmax(ylim[1], pmin(ylim[2], py)), log = log, 

            pch = ifelse(py < ylim[1], 6, ifelse(py > ylim[2], 

                2, 20)), cex = cex, col = col, xlab = xlab, ylab = ylab, 

            ylim = ylim, ...)

        abline(h = 0, lwd = 4, col = linecol)

    }

    .local(object, ...)

}

<environment: namespace:DESeq2>

Signatures:

        object        

target  "DESeqDataSet"

defined "DESeqDataSet"

Reference: http://stackoverflow.com/questions/5937832/r-show-source-code-of-an-s4-function-in-a-package