GSEA_run {TFEA.ChIP} | R Documentation |
Function to run a GSEA to analyze the distribution of TFBS across a sorted list of genes.
GSEA_run(gene.list, LFC, chip_index = get_chip_index(), get.RES = FALSE, RES.filter = NULL)
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. |
a list of: Enrichment.table: data frame containing accession ID, Cell type, ChIP-Seq treatment, transcription factor tested, enrichment score, 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.
data('hypoxia',package = 'TFEA.ChIP') 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)