getAgeR: Wrapper to retrieve any of various age estimates from...

In metamaden/cgageR:

Description

Use up to four methods to estimate sample age based on Beta-value methylation data.

Usage

getAgeR(df, epitoc=FALSE, horvath=FALSE, hannum=FALSE, drift=FALSE, driftcg=NULL, chrage=NULL, showStatusHannum=FALSE, keepres=FALSE,keepcpgs.hannum=TRUE,
       keepcpgs.epitoc=TRUE,keepcpgs.horvath=TRUE)

Arguments

df	Beta-value data frame, where columns are samples and rows are markers.
epitoc	Uses the epiTOC algorithm to estimate age in terms of mean Beta-value methylation.
horvath	Uses Horvaths human CpG clock, as implemented in wateRmelon, to estimate sample age.
hannum	Uses Hannums human CpG clock from blood to estimate sample age.
drift	Uses user-provided drift CpG methylation to determine mean of residuals across drifting CpGs.
driftcg	List of drifting CpG marker IDs to use if drift is TRUE.
chrage	Numeric vector of chronologic (patient) age, in same order as columns in df.
showStatusHannum	Whether to display status of Hannum clock calculations.
keepres	Whether to retain residuals for individual drift CpGs.
keepcpgs.epitoc	Whether to retain list of CpGs from epiTOC used for calculation.
keepcpgs.hannum	Whether to retain list of CpGs from Hannum clock used for calculation.
keepcpgs.horvath	Whether to retain list of CpGs from Horvath clock used for calculation.

Value

Returns a list of specified age estimates and affiliated output.

Author(s)

Sean K Maden

References

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

2. Horvath et al. "DNA methylation age of humna tissues and cell typesw." Genome Biology, 2013.

3. Pidsley et al. "A data-driven approach to preprocessing Illumina 450K methylation array data." BMC Genomics, 2013.

4. Yang et al. "Correlation of an epigenetic mitotic clock with cancer risk." Genome Biology, 2016.

Examples

# require(wateRmelon); data(melon)
bval <- betas(melon)
est.ages <- getAgeR(bval,epitoc=TRUE,horvath=TRUE,hannum=TRUE,drift=FALSE,showStatusHannum=TRUE,
                    keepcpgs.epitoc=TRUE,keepcpgs.hannum=TRUE,keepres=FALSE,chrage=NULL)

## The function is currently defined as
getAgeR <- function(df,epitoc=FALSE,horvath=FALSE,hannum=FALSE,drift=FALSE,driftcg,chrage,
                    keepres=FALSE,showStatusHannum=TRUE,keepcpgs.epitoc=TRUE,keepcpgs.hannum=TRUE,
                   keepcpgs.horvath=TRUE){
  returnlist <- c()

  if(epitoc){
    message("Getting epiTOC age estimates...")
    tocout <- getEpiTOC(df)
    returnlist <- append(returnlist,tocout,keepcpgs.epitoc)
    names(returnlist)[[length(returnlist)]] <- "epiTOC.Age.Estimates"
    message("Done! Continuing...")
  }

  if(horvath){
    suppressMessages(require(wateRmelon))
    message("Getting Horvath age estimates...")
    horvout <- as.data.frame(agep(df)); colnames(horvout)<-"Horvath.Est"
    if(keepcpgs.horvath){
      int.horvath <- intersect(rownames(df),HorvathLongCGlist[,1])
      horvout <- list(horvout,list(int.horvath))
      names(horvout)[[2]] <- "Horvath.CpGs.Used"
    }
    returnlist <- append(returnlist,list(horvout))
    names(returnlist)[[length(returnlist)]] <- "HorvathClock.output"
    message("Done! Continuing...")
  }
       
  if(hannum){
    hannout <- getHannumEst(df)
    returnlist <- append(returnlist,hannout,keepcpgs.hannum,showStatusHannum)
    names(returnlist)[[length(returnlist)]] <- "Hannum.Clock.Age.Estimates"
  }

  if(drift){
    driftout <- getDrift(df,driftcg,chrage,keepres)
    names(returnlist)[[length(returnlist)]] <- "Drift.Age.Estimates"
  }
  message("Age estimation complete. Returning..")
return(returnlist)
}

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