ge_gsea: ge_gsea

In oriolarques/GEGVIC: A workflow to analyse Gene Expression, Genetic Variations and Immune cell Composition of tumour samples using Next Generation Sequencing data.

ge_gsea

Description

Performs Gene Set Enrichment Analysis using gene sets specified by the user.

Usage

ge_gsea(annot_res, gmt, gsea_pvalue = 0.2)

Arguments

annot_res	The output of ge_annot. List containing data frames of differential gene expression results between the different groups.
gmt	Path to the gmt file that contain the gene sets of interest.
gsea_pvalue	Numeric value to define the adjusted pvalue cutoff during GSEA. Set to 0.2 by default.

Value

Returns ggplot objects and a list of gseaResult objects.

Examples

results.dds <- ge_diff_exp(counts = sample_counts,
                           genes_id = 'ensembl_gene_id',
                           metadata = sample_metadata,
                           design = 'MSI_status',
                           ref_level = c('MSI_status', 'MSS'),
                           shrink = 'apeglm')
annot.res <- ge_annot(results_dds = results_dds,
                      genes_id = 'ensembl_gene_id',
                      biomart = ensembl_biomart_GRCh38_p13)
gsea.res <- ge_gsea(annot_res = annot.res,
                    gmt = 'inst/extdata/c2.cp.reactome.v7.5.1.symbols.gmt',
                    gsea_pvalue = 0.2)

oriolarques/GEGVIC documentation built on Oct. 30, 2024, 10:44 p.m.