#1.TissueEnrich

BiocManager::install("TissueEnrich")
library(TissueEnrich)
library(SummarizedExperiment)
#data<-system.file("extdata", "test.expressiondata.txt", package = "TissueEnrich")

expressionData<-read.csv("714.csv",header=TRUE,row.names=1)

#expressionData<-read.table(data,header=TRUE,row.names=1,sep='\t')

se<-SummarizedExperiment(assays = SimpleList(as.matrix(expressionData)),rowData = row.names(expressionData),colData = colnames(expressionData))
output<-teGeneRetrieval(se,foldChangeThreshold = 5,
                        maxNumberOfTissues = 7, expressedGeneThreshold = 1)
#foldChangeThreshold: A numeric Threshold of fold change, default 5.
#maxNumberOfTissues: A numeric Maximum number of tissues in a group for group enriched genes, default 7.
#expressedGeneThreshold: A numeric Minimum gene expression cutoff for the gene to be called as expressed, default 1.


head(assay(output))

DATA=assay(output)

write.table(DATA,file="SEGS.txt",sep = "\t",col.names = T)

teGeneRetrieval: Identification of tissue-specific genes

The teGeneRetrieval function is used to define tissue-specific genes, using the algorithm from the HPA (Uhlén et al. 2015). It takes an SummarizedExperiment object containing expression information as input (rows as genes and columns as tissue) and classifies the genes into different gene groups and returns the information in another SummarizedExperiment object. The users also have the options of changing the default thresholds to vary the degree of tissue specificity of genes. More details about the gene groups and HPA thresholds are provided below.

Gene groups
The genes are divided into six groups based on their gene expression across the tissues. These groups are:

Not Expressed: Genes with an expression level less than 1 (TPM or FPKM) across all the tissues.
Tissue Enriched: Genes with an expression level greater than or equal to 1 (TPM or FPKM) that also have at least five-fold higher expression levels in a particular tissue compared to all other tissues.
Group Enriched: Genes with an expression level greater than or equal to 1 (TPM or FPKM) that also have at least five-fold higher expression levels in a group of 2-7 tissues compared to all other tissues, and that are not considered Tissue Enriched.
Tissue Enhanced: Genes with an expression level greater than or equal to 1 (TPM or FPKM) that also have at least five-fold higher expression levels in a particular tissue compared to the average levels in all other tissues, and that are not considered Tissue Enriched or Group Enriched.
Expressed in all: Genes with an expression level greater than or equal to 1 (TPM or FPKM) across all of the tissues that are not in any of the above 4 groups.
Mixed: Genes that are not assigned to any of the above 5 groups.
Genes from the Tissue Enriched, Group Enriched, and Tissue Enhanced groups are classified as tissue-specific genes.

#2.SEGtool
install.packages('https://cran.r-project.org/src/contrib/Archive/hwriterPlus/hwriterPlus_1.0-3.tar.gz', repos=NULL, type='source')
install.packages("TeachingDemos")
library(SEGtool)
SEGtool_result <- SEGtool (expressionData, exp_cutoff = 1,multi_cpu = 4, detect_mod=2,
                           result_outdir='SEGtool_result', draw_heatmap=TRUE, draw_pca=TRUE, draw_plot=TRUE,
                           html_report=TRUE)