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Make_expressionset.Rmd
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---
title: "R Notebook"
output: html_notebook
---
Rscript -e "rmarkdown::render('Make_expressionset.Rmd')"
Loading packages
```{r loading packages, message = F, warning = F}
library(wrapr)
library(data.table)
library(Biobase)
rm(list=ls())
```
Reading gene expression values for brain regions
```{r Reading gene expression values for brain regions}
# BM10
expr_bm10 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.BM_10.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.tsv", data.table = F)
row.names(expr_bm10) <- expr_bm10[[1]]
fdata_bm10 <- expr_bm10[, c(1, 2)]
expr_bm10 <- expr_bm10[, -c(1, 2)]
# BM22
expr_bm22 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.BM_22.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.tsv", data.table = F)
row.names(expr_bm22) <- expr_bm22[[1]]
fdata_bm22 <- expr_bm22[, c(1, 2)]
expr_bm22 <- expr_bm22[, -c(1, 2)]
# BM36
expr_bm36 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.BM_36.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.tsv", data.table = F)
row.names(expr_bm36) <- expr_bm36[[1]]
fdata_bm36 <- expr_bm36[, c(1, 2)]
expr_bm36 <- expr_bm36[, -c(1, 2)]
# BM44
expr_bm44 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.BM_44.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.tsv", data.table = F)
row.names(expr_bm44) <- expr_bm44[[1]]
fdata_bm44 <- expr_bm44[, c(1, 2)]
expr_bm44 <- expr_bm44[, -c(1, 2)]
# ROSMAP
expr_ros <- readRDS("/sc/orga/projects/zhangb03a/shared/ROSMAP/Synapse/RNAseq/covariates_adjustment/expression.log2FPKM.batch_pmi_msex_RIN_adj.no_outliers.symbol_clean.RDS")
# Mayo TCX
expr_mayo_tcx <- fread("/sc/orga/projects/zhangb03a/shared/Mayo/RNASeq/Reprocessing/normalization/Mayo.TCX.log2CPM.sc_RIN_sex_flowcell_Adj.tsv", data.table = F)
row.names(expr_mayo_tcx) <- expr_mayo_tcx[[1]]
fdata_mayo_tcx <- expr_mayo_tcx[, c(1, 2)]
expr_mayo_tcx <- expr_mayo_tcx[, -c(1:6)]
# Mayo CBE
expr_mayo_cbe <- fread("/sc/orga/projects/zhangb03a/shared/Mayo/RNASeq/Reprocessing/normalization/Mayo.CBE.log2CPM.sc_RIN_sex_flowcell_Adj.tsv", data.table = F)
row.names(expr_mayo_cbe) <- expr_mayo_cbe[[1]]
fdata_mayo_cbe <- expr_mayo_cbe[, c(1, 2)]
expr_mayo_cbe <- expr_mayo_cbe[, -c(1:6)]
```
Reading meta for brain regions
```{r Reading meta for brain regions}
#BM10
meta_bm10 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.meta.BM_10.tsv", data.table = F)
# adding row names
rownames(meta_bm10) <- meta_bm10$Sampleid
# adding severity column
meta_bm10$severity <- ifelse(meta_bm10$CDR == 0.5, "MCI", ifelse(meta_bm10$CDR == 0, "NL", "Severe"))
#BM22
meta_bm22 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.meta.BM_22.tsv", data.table = F)
# adding row names
rownames(meta_bm22) <- meta_bm22$Sampleid
# adding severity column
meta_bm22$severity <- ifelse(meta_bm22$CDR == 0.5, "MCI", ifelse(meta_bm22$CDR == 0, "NL", "Severe"))
#BM36
meta_bm36 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.meta.BM_36.tsv", data.table = F)
# adding row names
rownames(meta_bm36) <- meta_bm36$Sampleid
# adding severity column
meta_bm36$severity <- ifelse(meta_bm36$CDR == 0.5, "MCI", ifelse(meta_bm36$CDR == 0, "NL", "Severe"))
#BM44
meta_bm44 <- fread("/sc/orga/projects/zhangb03a/shared/msbb-seq/Data/mixed_model_correction_updated/msbb.meta.BM_44.tsv", data.table = F)
# adding row names
rownames(meta_bm44) <- meta_bm44$Sampleid
# adding severity column
meta_bm44$severity <- ifelse(meta_bm44$CDR == 0.5, "MCI", ifelse(meta_bm44$CDR == 0, "NL", "Severe"))
# adding severity column
pData(expr_ros)$severity <- ifelse((pData(expr_ros)$cogdx == 2 | pData(expr_ros)$cogdx == 3), "MCI", ifelse(pData(expr_ros)$cogdx < 2, "NL", "Severe"))
# Mayo TCX
meta_mayo_tcx <- fread("/sc/orga/projects/zhangb03a/shared/Mayo/RNASeq/Reprocessing/normalization/Mayo.TCX.meta.tsv", data.table = F)
meta_mayo_tcx$AgeAtDeath <- as.numeric(gsub("_or_above", "", meta_mayo_tcx$AgeAtDeath))
colnames(meta_mayo_tcx)[7] <- "AOD"
rownames(meta_mayo_tcx) <- meta_mayo_tcx$SampleID
# Mayo CBE
meta_mayo_cbe <- fread("/sc/orga/projects/zhangb03a/shared/Mayo/RNASeq/Reprocessing/normalization/Mayo.CBE.meta.tsv", data.table = F)
meta_mayo_cbe$AgeAtDeath <- as.numeric(gsub("_or_above", "", meta_mayo_cbe$AgeAtDeath))
colnames(meta_mayo_cbe)[7] <- "AOD"
rownames(meta_mayo_cbe) <- meta_mayo_cbe$SampleID
```
Making expressionset for MSBB data
```{r Making expressionset for MSBB data}
# Checking if sample orders are same between expr and meta
annot_ls <- list(fdata_bm10, fdata_bm22, fdata_bm36, fdata_bm44, fdata_mayo_tcx, fdata_mayo_cbe)
meta_ls <- list(meta_bm10, meta_bm22, meta_bm36, meta_bm44, meta_mayo_tcx, meta_mayo_cbe)
expr_ls <- list(expr_bm10, expr_bm22, expr_bm36, expr_bm44, expr_mayo_tcx, expr_mayo_cbe)
expr_ls <- lapply(expr_ls, as.matrix)
mapply(function(x, y) identical(rownames(x), colnames(y)), meta_ls, expr_ls)
# making expressionset
pheno_msbb_mayo <- lapply(meta_ls, function(x) new("AnnotatedDataFrame", data = x))
feature_msbb_mayo <- lapply(annot_ls, function(x) new("AnnotatedDataFrame", data = x))
exprset_msbb_mayo <- mapply(function(x, y, z) ExpressionSet(assayData = x, phenoData = y, featureData = z), expr_ls, pheno_msbb_mayo, feature_msbb_mayo, SIMPLIFY = F)
# putting all expressionset in one list
exprset_all <- c(exprset_msbb_mayo, expr_ros)
```
Writing results
```{r Writing results}
invisible(mapply(saveRDS, exprset_all, paste0("/sc/orga/projects/zhangb03a/lei_guo/Expressionset_MSBB_ROSMAP_Mayo/Expressionset/", c("Exprset.BM_10.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.RDS", "Exprset.BM_22.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.RDS", "Exprset.BM_36.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.RDS", "Exprset.BM_44.PMI_race_sex_RIN_exonicRate_rRnaRate_batch_adj.RDS", "Exprset.Mayo.TCX.log2CPM.sc_RIN_sex_flowcell_Adj.RDS", "Exprset.Mayo.CBE.log2CPM.sc_RIN_sex_flowcell_Adj.RDS", "Exprset.ROSMAP_log2FPKM.batch_pmi_msex_RIN_adj.no_outliers.symbol_clean.RDS"))))
```