calculate_pathway_gsea | R Documentation |

Convert expression matrix to GSEA pathway scores (would take a similar place in workflow before average_clusters/binarize)

calculate_pathway_gsea( mat, pathway_list, n_perm = 1000, scale = TRUE, no_warnings = TRUE )

`mat` |
expression matrix |

`pathway_list` |
a list of vectors, each named for a specific pathway, or dataframe |

`n_perm` |
Number of permutation for fgsea function. Defaults to 1000. |

`scale` |
convert expr_mat into zscores prior to running GSEA?, default = FALSE |

`no_warnings` |
suppress warnings from gsea ties |

matrix of GSEA NES values, cell types as row names, pathways as column names

gl <- list( "n" = c("PPBP", "LYZ", "S100A9"), "a" = c("IGLL5", "GNLY", "FTL") ) pbmc_avg <- average_clusters( mat = pbmc_matrix_small, metadata = pbmc_meta, cluster_col = "classified" ) calculate_pathway_gsea( mat = pbmc_avg, pathway_list = gl )

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