Calculation of immune and stromal scores in tumor microenvironment
To use ISTMEscore package, you can download Binary package named "ISTMEscore_1.0.0.zip" for Windows or Source package named "ISTMEscore_1.0.0.tar.gz" for Linux and Windows. Next, you could install this package with the following codes in R：
install.packages("File path/ISTMEscore_1.0.0.tar.gz", repos = NULL, type = "source")
or for Windows:
install.packages("File path/ISTMEscore_1.0.0.zip", repos = NULL, type = "win.binary")
then
library(ISTMEscore)
The ISTMEscore consists of the four functions, including ISTMEscore_read, ISTMEscore_score, ISTMEscore_subtype and ISTMEscore_SSEA functions. The ISTMEscore_read function is used to read transcriptome from GEO database. The ISTMEscore_score is used to calculate our immune and stromal scores. The ISTMEscore_subtype is used to identify the four tumor microenvironment subtypes based on Zeng's study. The ISTMEscore_SSEA is used to identify genes highly expressed in specific TME subtypes (See Methods_SSEA.pdf for details). See Function annotation folder for parameter annotations for each ISTMEscore function.
The sample data are downloaded in https://ftp.ncbi.nlm.nih.gov/geo/series/GSE50nnn/GSE50081/matrix/GSE50081_series_matrix.txt.gz (GSE50081_series_matrix.txt.gz) and https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL570 (GPL570-55999.txt)
data=ISTMEscore_read(inputdata="data/GSE50081_series_matrix.txt.gz", GPL="data/GPL570-55999.txt", rank_col=F, rank_row=F, log2=F, z_score=F, min_max=F, datatype="chip_matrix", aggregatemethod="max", probe_first=T,Ngene=11)
score=ISTMEscore_score(data)
group=ISTMEscore_subtype(data)
SSEA_gene=ISTMEscore_SSEA(data,group,multigroup=F,threshold_anova_p=0.001,nPerm=100)
Please cite "Zeng (J Trans Med, 2021). Immune and Stromal Scoring System Associated with Tumor Microenvironment and Prognosis: A Gene-Based Multi-Cancer Analysis"