bioinformatic-analysis / istmescore

Calculation of immune and stromal scores in tumor microenvironment

ISTMEscore

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.

Data reading

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)

Calculation of immune and stromal scores

score=ISTMEscore_score(data)

Identification of TME subtypes

group=ISTMEscore_subtype(data)

identify genes highly expressed in specific TME subtypes

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"