Nothing
## ---- 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()
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