getHannum: Get sample age estimates using Hannum CpG Methylation Clock...

In metamaden/cgageR:

Description

Uses methylation and coefficients at specified CpGs to estimate sample age as described in Hannum et al 2013.

Usage

getHannum(df, keepcpgs.hannum=TRUE, showStatusHannum=TRUE)

Arguments

df	Beta-value data frame, with samples as columns and markers as rows.
keepcpgs.hannum	Wether to retain list of CpGs used (model CpGs available in provided df).
showStatusHannum	Whether to display detailed status of age estimate calculations.

Author(s)

Sean Maden

References

Hannum et al. "Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates." Molecular Cell, 2014.

Examples

## The function is currently defined as
function (df, keepcpgs.hannum=TRUE, showStatusHannum=TRUE) 
{
    message("Initializing Hannum Clock age estimates...")
    hcgs <- hannumModel$marker
    int.hcgs <- rownames(df[rownames(df) 
    vector.df <- as.data.frame(matrix(nrow = ncol(df), ncol = (length(int.hcgs) + 
        1)))
    colnames(vector.df) <- c(int.hcgs, "Est.Age")
    rownames(vector.df) <- colnames(df)
    for (i in 1:nrow(vector.df)) {
        for (j in 1:(ncol(vector.df) - 1)) {
            cgi <- colnames(vector.df)[j]
            hcgs.weighti <- hannumModel[hannumModel$marker == 
                cgi, ]$coefficient
            vector.df[i, j] <- df[cgi, i] * hcgs.weighti
        }
        vector.df$Est.Age[i] <- sum(vector.df[i, 1:(ncol(vector.df) - 
            3)])
        if (showStatusHannum) {
 #           message("Hannum Age Est. Status: Finished sample ",i," or ",round(100*(i/nrow(vector.df)),3),"%")
        }
    }
    dfhan <- data.frame(Hannum.Est = vector.df$Est.Age)
    return.list <- list(dfhan)
    names(return.list) <- "Hannum.Clock.Est"
    if (keepcpgs.hannum) {
        return.list <- append(return.list, list(rownames(df[rownames(df) 
            hcgs, ])))
        names(return.list)[[length(return.list)]] <- "Hannum.CpGs.Used"
    }
    return(return.list)
}

metamaden/cgageR documentation built on May 20, 2019, 5:07 p.m.