##' A universal enrichment analyzer
##'
##'
##' @title enricher
##' @param gene a vector of gene id
##' @param pvalueCutoff pvalue cutoff
##' @param pAdjustMethod one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
##' @param universe background genes
##' @param minGSSize minimal size of genes annotated for testing
##' @param maxGSSize maximal size of genes annotated for testing
##' @param qvalueCutoff qvalue cutoff
##' @param TERM2GENE user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
##' @param TERM2NAME user input of TERM TO NAME mapping, a data.frame of 2 column with term and name
##' @return A \code{enrichResult} instance
##' @author Guangchuang Yu
##' @export
enricher <- function(gene,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe,
minGSSize=10,
maxGSSize=500,
qvalueCutoff = 0.2,
TERM2GENE,
TERM2NAME = NA) {
USER_DATA <- build_Anno(TERM2GENE, TERM2NAME)
enricher_internal(gene = gene,
pvalueCutoff = pvalueCutoff,
pAdjustMethod = pAdjustMethod,
universe = universe,
minGSSize = minGSSize,
maxGSSize = maxGSSize,
qvalueCutoff = qvalueCutoff,
USER_DATA = USER_DATA)
}
##' a universal gene set enrichment analysis tools
##'
##'
##' @title GSEA
##' @param geneList order ranked geneList
##' @param exponent weight of each step
##' @param nPerm number of permutations
##' @param minGSSize minimal size of each geneSet for analyzing
##' @param maxGSSize maximal size of genes annotated for testing
##' @param pvalueCutoff pvalue cutoff
##' @param pAdjustMethod p value adjustment method
##' @param TERM2GENE user input annotation of TERM TO GENE mapping, a data.frame of 2 column with term and gene
##' @param TERM2NAME user input of TERM TO NAME mapping, a data.frame of 2 column with term and name
##' @param verbose logical
##' @param seed logical
##' @param by one of 'fgsea' or 'DOSE'
##' @return gseaResult object
##' @author Guangchuang Yu
##' @export
GSEA <- function(geneList,
exponent = 1,
nPerm = 1000,
minGSSize = 10,
maxGSSize = 500,
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
TERM2GENE,
TERM2NAME = NA,
verbose = TRUE,
seed = FALSE,
by = 'fgsea') {
USER_DATA <- build_Anno(TERM2GENE, TERM2NAME)
GSEA_internal(geneList = geneList,
exponent = exponent,
nPerm = nPerm,
minGSSize = minGSSize,
maxGSSize = maxGSSize,
pvalueCutoff = pvalueCutoff,
pAdjustMethod = pAdjustMethod,
verbose = verbose,
USER_DATA = USER_DATA,
seed = seed,
by = by)
}
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