Example_code/2.2.iPSC-derived_chondrocytes.R

In GuangshengPei/deCS: Cell type enrichment analysis

setwd("downloaded/deCS-master")

# Load the bulk RNA-seq datasets and data preprocess
data = read.delim("Example_data/2.2.iPSC-derived_chondrocytes/Chondrocytes_TPM.txt", head = T)
tag_temp = names(table(data$Symbol)[table(data$Symbol) > 1])
tag = as.character(data$Symbol[!(data$Symbol %in% tag_temp)])
data = data[which(data$Symbol %in% tag),]
rownames(data) = data$Symbol
data = data[, -1]
data_clean <- data[which(apply(data, 1, max) > 1),]

# Bulk RNA-seq normalization
library(deTS)
data(correction_factor)
Chondrocytes_normalized = tsea.expression.normalization(data_clean, correction_factor, normalization = "abundance")

# deCS annotation
library(deCS)
data(BlueprintEncode_fine)
Chondrocytes_BlueprintEncode_fine_cor = deCS.correlation(Chondrocytes_normalized, BlueprintEncode_fine_t_score, methods = "spearman", ref_panel_markers_ratio = 0.05, cor_threshold = 0.1, cell_type_threshold = 0.1)