GSEA_run {TFEA.ChIP} | R Documentation

## Function to run a GSEA analysis

### Description

Function to run a GSEA to analyze the distribution of TFBS across a sorted list of genes.

### Usage

    GSEA_run(
      gene.list,
      LFC,
      chip_index = get_chip_index(),
      get.RES = FALSE,
      RES.filter = NULL,
      perms = 1000
    )

### Arguments

`gene.list` | List of Entrez IDs ordered by their fold change.
`LFC` | Vector of log2( Fold Change ) values.
`chip_index` | Output of the function “get_chip_index”, a data frame containing accession IDs of ChIPs on the database and the TF each one tests. If not provided, the whole internal database will be used
`get.RES` | (Optional) boolean. If TRUE, the function stores Running Enrichment Scores of all/some TF.
`RES.filter` | (Optional) chr vector. When get.RES==TRUE, allows to choose which TF's Running Enrichment Score to store.
`perms` | Number of permutations for a permutation test.

### Value

a list of: Enrichment.table: data frame containing accession ID, Cell type, ChIP-Seq treatment, transcription factor tested, enrichment score, raw and adjusted p-value, and argument of every ChIP-Seq experiment. RES (optional): list of running sums of every ChIP-Seq indicators (optional): list of 0/1 vectors that stores the matches (1) and mismatches (0) between the gene list and the gene set.

### Examples

    data('hypoxia',package = 'TFEA.ChIP')
    hypoxia <- preprocessInputData(hypoxia)
    chip_index<-get_chip_index(TFfilter = c('HIF1A','EPAS1','ARNT'))
    GSEA.result <- GSEA_run( hypoxia$Genes, hypoxia$log2FoldChange, chip_index, get.RES = TRUE)

[Package TFEA.ChIP version 1.12.0 Index]