R/base_stackFragment.R

In dpeak: dPeak (Deconvolution of Peaks in ChIP-seq Analysis)

# stack fragment (projection to coordinates)

.stackFragment <- function( fragmentMat ) {

    if ( !is.na(fragmentMat[1,1]) ) {
        xvarq <- c( min(fragmentMat[,1]), max(fragmentMat[,2]) )
        xvar <- c(seq(from = xvarq[1], to = xvarq[2]))
        yvar <- .ff_stack( fragmentMat[,1], fragmentMat[,2], xvarq[1], xvarq[2] )

        outMat <- cbind( xvar, yvar )
    } else {
        outMat <- matrix( NA )
    }

    return( outMat )
}