The goal of GSVAutils is to provide severall functions used in TIGS project.
remotes::install_github("GSVAutils")This is a basic example which shows you how to run GSVA.
library(GSVAutils)
#> Warning: replacing previous import 'Biobase::combine' by 'dplyr::combine' when
#> loading 'GSVAutils'
## basic example code
data("example_gsets")
data("example_data")
ExprList = GenTibbleList(list(example_data))
#> Find nothing about gene symbol in fData, try search it...
#> Find gene_assignment
#> Processing...
#> Done.
res <- ApplyGSVA(example_gsets,
group_col = "Cell_type",
gene_col = "Symbol", ExprMatList = ExprList, method = "gsva")
#> Estimating GSVA scores for 21 gene sets.
#> Computing observed enrichment scores
#> Estimating ECDFs with Gaussian kernels
#> Using parallel with 8 cores
#>
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|======================================================================| 100%More about GSVA please run ?GSVA::gsva in R console.