## ---- echo = FALSE------------------------------------------------------------ knitr::opts_chunk$set(comment = "", message=FALSE, warning = FALSE) ## ----eval = FALSE------------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("RNAAgeCalc") ## ----------------------------------------------------------------------------- library(RNAAgeCalc) ## ----------------------------------------------------------------------------- data(fpkmExample) head(fpkm) ## ----message = TRUE----------------------------------------------------------- chronage = data.frame(sampleid = colnames(fpkm), age = c(30,50)) res = predict_age(exprdata = fpkm, tissue = "brain", exprtype = "FPKM", chronage = chronage) head(res) ## ----------------------------------------------------------------------------- # This example is just for illustration purpose. It does not represent any # real data. # construct a large gene expression data fpkm_large = cbind(fpkm, fpkm+1, fpkm+2, fpkm+3) fpkm_large = cbind(fpkm_large, fpkm_large, fpkm_large, fpkm_large) colnames(fpkm_large) = paste0("sample",1:32) # construct the samples' chronological age chronage2 = data.frame(sampleid = colnames(fpkm_large), age = 31:62) res2 = predict_age(exprdata = fpkm_large, exprtype = "FPKM", chronage = chronage2) head(res2) ## ----message = FALSE---------------------------------------------------------- library(SummarizedExperiment) colData = data.frame(age = c(40, 50)) se = SummarizedExperiment(assays=list(FPKM=fpkm), colData=colData) res3 = predict_age_fromse(se = se, exprtype = "FPKM") head(res3) ## ----------------------------------------------------------------------------- makeplot(res2) ## ----sessionInfo-------------------------------------------------------------- sessionInfo()