GenePermGSEA: Gene permuting GSEA with or without filtering by absolute GSEA.

Description

Gene-set enrichment analysis (GSEA) is popularly used to assess the enrichment of differential signal in a pre-defined gene-set without using a cutoff threshold for differential expression. The significance of enrichment is evaluated through sample- or gene-permutation method. Although the sample-permutation approach is highly recommended due to its good false positive control, we must use gene-permuting method if the number of samples is small. However, such gene-permuting GSEA (or preranked GSEA) generates a lot of false positive gene-sets as the inter-gene correlation in each gene set increases. These false positives can be successfully reduced by filtering with the one-tailed absolute GSEA results. This package provides a function that performs gene-permuting GSEA calculation with or without the absolute filtering. Without filtering, users can perform (original) two-tailed or one-tailed absolute GSEA.

Usage

GenePermGSEA(countMatrix, GeneScoreType, idxCase, idxControl, GenesetFile, normalization, minGenesetSize = 10, maxGenesetSize = 300, q = 1, nPerm = 1000, GSEAtype = "absFilter", FDR = 0.05, FDRfilter = 0.05, minCount = 3)

Arguments

countMatrix

Normalized RNA-seq read count matrix.

GeneScoreType

Type of gene score. Possible gene score is "moderated_t","SNR", "FC" (log fold change score) or "RANKSUM" (zero centered).

idxCase

Indices for case samples in the count matrix. e.g., 1:3

idxControl

Indices for control samples in the count matrix. e.g., 4:6

GenesetFile

File path for gene set file. Typical GMT file or its similar 'tab-delimited' file is available. e.g., "C:/geneset.gmt"

normalization

Type 'DESeq' if the input matrix is composed of raw read counts. It will normalize the raw count data using DESeq method. Or type 'AlreadyNormalized' if the input matrix is already normalized.

minGenesetSize

Minimum size of gene set allowed. Gene-sets of which sizes are below this value are filtered out from the analysis. Default = 10

maxGenesetSize

Maximum size of gene set allowed. Gene-sets of which sizes are larger this value are filtered out from the analysis. Default = 300

Weight exponent for gene score. For example, if q=0, only rank of gene score is reflected in calculating gene set score (preranked GSEA). If q=1, the gene score itself is used. If q=2, square of the gene score is used.

nPerm

The number of gene permutation. Default = 1000.

GSEAtype

Type of GSEA. Possible value is "absolute", "original" or "absFilter". "absolute" for one-tailed absolute GSEA. "original" for the original two-tailed GSEA. "absFilter" for the original GSEA filtered by the results from the one-tailed absolute GSEA.

FDR

FDR cutoff for the original or absolute GSEA. Default = 0.05

FDRfilter

FDR cutoff for the one-tailed absolute GSEA for absolute filtering (only working when GSEAtype is "absFilter"). Default = 0.05

minCount

Minimum median count of a gene to be included in the analysis. It is used for gene-filtering to avoid genes having small read counts. Default = 0

Value

GSEA result table sorted by FDR Q-value.

Source

Nam, D. Effect of the absolute statistic on gene-sampling gene-set analysis methods. Stat Methods Med Res 2015. Subramanian, A., et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. P Natl Acad Sci USA 2005;102(43):15545-15550. Li, J. and Tibshirani, R. Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-Seq data. Statistical Methods in Medical Research 2013;22(5):519-536.

Details

Typical usages are GenePermGSEA(countMatrix = countMatrix, GeneScoreType = "moderated_t", idxCase = 1:3, idxControl = 4:6, GenesetFile = 'geneset.txt', GSEAtype = "absFilter")

References

Examples

Run this code


data(example)

# Create a gene set file and save it to your local directory.
# Note that you can use your local gene set file (tab-delimited like *.gmt file from mSigDB).
# But here, we will generate a toy gene set file to show the structure of this gene set file.
# It consists of 100 gene sets and each contains 50 genes.

for(Geneset in 1:100)
{
  GenesetName = paste("Geneset", Geneset, sep = "_")
  Genes = paste("Gene", (Geneset*100-99):(Geneset*100), sep="", collapse = '\t')
  Geneset = paste(GenesetName, Genes, sep = '\t')
  write(Geneset, file = "geneset.txt", append = TRUE, ncolumns = 1)
}

# Run Gene-permuting GSEA
RES = GenePermGSEA(countMatrix = example, GeneScoreType = "moderated_t", idxCase = 1:3,
                    idxControl = 4:6, GenesetFile = 'geneset.txt', normalization = 'DESeq',
                    GSEAtype = "absFilter")
RES

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