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Copy pathGTEx_control_age_prediction.R
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GTEx_control_age_prediction.R
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library(RNAAgeCalc)
library(readr)
library(ggplot2)
library(tidyverse)
library(tibble)
library(dplyr)
library(ggpubr)
library(extrafont)
library(ggsci)
library(ggthemes)
library(data.table)
library('recount')
url <- download_study('SRP012682')
load(file.path('SRP012682', 'rse_gene.Rdata'))
## Scale counts
rse <- scale_counts(rse_gene)
counts_brain <- rse@assays@data@listData[["counts"]]
write.csv(counts_brain,"(GTEX_data1.csv" )
rcounts <- read.csv("(GTEX_data1.csv")
new_data <- rcounts[ c( "SRR1069188", "SRR1071289",
"SRR1071880",
"SRR1072178",
"SRR1072367",
"SRR1072504",
"SRR1081741",
"SRR1084842",
"SRR1085495",
"SRR1310136",
"SRR1313642",
"SRR1316254",
"SRR1320071",
"SRR1335400")]
namesdata <- rcounts [1]
rawcounts <- read_xlsx("Book1.xlsx")
rnamesversionfree <-pivot_longer(namesdata, cols = everything()) %>%
separate(value, into = c('gene_id', 'beta'), sep = "\\.") %>%
select(-name)
rnames <- rnamesversionfree[,1]
rnamesdata <- as.data.frame(rnames)
rawnamesdataunique <-make.names(rnamesdata[,1], unique = TRUE)
row.names(new_data) <- rawnamesdataunique
cp <- predict_age(
new_data,
tissue = c("brain"),
exprtype = c("counts"),
idtype = c("ENSEMBL"),
stype = c("all"),
signature = NULL,
genelength = NULL,
chronage = NULL,
maxp = NULL
)
write.csv(cp,"GTEX_RNAAGE.csv" )
Agerange <- t(data.frame(35,55,45,65,65,65,55,65,65,45,45,75,75,25 ))
df <- rownames_to_column(Agerange, var = "X")
Age_r <- merge(Agerange,Sample_names)
Sample_names <- t(data.frame("SRR1335400",
"SRR1081741",
"SRR1084842",
"SRR1085495",
"SRR1069188",
"SRR1071289",
"SRR1071880",
"SRR1072178",
"SRR1072367",
"SRR1072504",
"SRR1310136",
"SRR1313642",
"SRR1316254",
"SRR1320071"
))
df3 <- (data.frame(names =c("SRR1069188"
,"SRR1071289"
,"SRR1071880"
,"SRR1072178"
,"SRR1072367"
,"SRR1072504"
,"SRR1081741"
,"SRR1084842"
,"SRR1085495",
"SRR1310136",
"SRR1313642"
,"SRR1316254"
,"SRR1320071"
,"SRR1335400"
), age =c(65,65,55,65,65,45,55,45,65,45,75,75,25,35 ),
RNAAGE = c(57.01823,
52.93410
,
41.68924
,
56.01721
,
55.07727
,
43.92025
,
47.60838
,
42.83530
,
59.59275
,
43.84962
,
54.96432
,
61.57459
,
22.29486
,
41.56827)))
df2 <- df1[-1]
rnames1 <- df1[,1]
rnamesdata1 <- as.data.frame(rnames1)
row.names(df2) <- rnamesdata1[1]
Happy <- data.frame(cp,c(
"SRR1081741",
"SRR1084842",
"SRR1085495",
"SRR1069188",
"SRR1071289",
"SRR1071880",
"SRR1072178",
"SRR1072367",
"SRR1072504",
"SRR1310136",
"SRR1313642",
"SRR1316254",
"SRR1320071",
"SRR1335400"))
setDT(Agerange)
#Plotting