R/base_selectModel.R

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

# choose optimal model

.selectModel <- function( BIC_vec, maxComp, pConst=0.2 ) {

    # remove models with NA

    gvec <- c(seq_len(maxComp))[ !is.na(BIC_vec) ]
    glen <- length(gvec)
    BIC_vec <- BIC_vec[ !is.na(BIC_vec) ]

    # find the first local min

    if ( glen <= 2 ) {
        # if length is shorter than two, just use min

        min_model <- gvec[ which.min(BIC_vec) ]
    } else {
        min_model <- gvec[1]

        diff_bic <- diff(BIC_vec)
        for ( k in seq(from = 2, to = (glen-1)) ) {
            if ( diff_bic[k-1] < 0 & diff_bic[k] > 0 ) {
                min_model <- gvec[k]
                break
            }
        }

        if ( min_model == gvec[1] & which.min(BIC_vec) == glen ) {
            min_model <- gvec[glen]
        }
    }

    # find the smallest model which is similar to the first local min

    if ( glen <= 2 | which( gvec == min_model ) == 1 ) {
        opt_model <- min_model
    } else {
        # cutoff to determine plateau

        cutoff <- ( max(BIC_vec) - min(BIC_vec) ) * pConst

        # search plateau

        loc_min <- which( gvec == min_model )

        k <- loc_min - 1
        while( k >= 1 ) {
            if ( abs( BIC_vec[loc_min] - BIC_vec[k] ) <= cutoff ) {
                loc_min <- k
                k <- loc_min - 1
            }
            k <- k - 1
        }

        opt_model <- gvec[loc_min]
    }

    return( opt_model )
}