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In this article, the editor introduces in detail "how to use ssGSEA.r in R language". The content is detailed, the steps are clear, and the details are handled properly. I hope this article "how to use ssGSEA.r in R language" can help you solve your doubts.

Gene set enrichment analysis of ssGSEA.r single sample

Usage: $Rscript.. / scripts/ssGSEA.r-husage:.. / scripts/ssGSEA.r [- h]-I expset-g geneset [- o outdir] [- p prefix] ssGSEA immunoinvasive assay optional arguments:-h,-- help show this help message and exit-I expset,-- expset expset input gene expression set matrix from RNA-seq data csv format [required]-g geneset -- geneset geneset input geneset database [required]-o outdir,-- outdir outdir output file directory [default cwd]-p prefix,-- prefix prefix output file name prefix [default demo] parameter description:

-I gene expression, it is recommended to use the standardized data of TPM:

IDTCGA-D7-A74A-01A-11R-A32D-31TCGA-BR-7704-01A-11R-2055-13TCGA-VQ-A91N-01A-11R-A414-31TCGA-CD-A4MH-01A-11R-A251-31NUP5018.6550531.5923228.2338228.76485CXCR464.85805125.12356.3524469.98976NT5E111.481869.858779.3738225.05824EFNA38.24785742.0330843.4643226.66024STC14.78111121.3632740.8107719.51568ZBTB7A95.51678103.4768158.3024126.2677CLDN91.1874562.4761380.3660817.347344

-g gene sets two columns of data, the first row of cell types and the second column of genes

The CellTypeSymbolB cellsMS4A1B cellsTCL1AB cellsMS4A1B cellsTCL1AB cellsHLA-DOBB cellsPNOCB cellsKIAA0125B cellsCD19B cellsCR2B cellsIGHG1B cellsFCRL2B cellsBLKB cellsIGHG1B cellsCOCHB cellsOSBPL10B cellsIGHA1B cellsTNFRSF17B cellsABCB4B cellsBLNK results show that:

Get the NES values of different gene sets in each sample:

NES value: standardizes the ssGSEA score with the absolute difference between the maximum and minimum values.

Cell_typeTCGA-B7-A5TK-01A-12R-A36D-31TCGA-BR-7959-01A-11R-2343-13TCGA-IN-8462-01A-11R-2343-13TCGA-BR-A4CR-01A-11R-A24K-31aDC0.6121305110.4527214220.4340650.352635B cells0.4233227750.4088700640.4266120.413857Blood vessels0.681023490.7754385720.6894330.577667CD8 T cells0.6756153850.6500732420.6291210.566048Cytotoxic cells0.6210561510.4252174420.4116170.3128DC0.6198389250.4850555790.4891010.266905Eosinophils0.5027849490.5149385570.4695410.488051iDC0.5316197560.498437210.5309310.390699Lymph Vessels0.7108427690.7213230720.6583910.500574 method description:

Single sample gene set enrichment analysis (single sample gene set enrichment analysis, ssGSEA) is an extension of GSEA method, which is mainly designed for single sample can not do GSEA. The article was published in nature in 2009 under the title Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1.

Firstly, the gene expression value of a given sample is standardized, and then the empirical cumulative distribution function is used to calculate the enrichment score (ES). Let the given gene set be G, the number of genes contained be NG, the number of genes contained in a single sample S, and the expression profile contain N genes whose absolute expression values are from high to low to determine the rank. I is assigned from 1 to N, and PGw and PNG are calculated accordingly.

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