RunGeneSetCollection_MSF: A function that runs analyzeGeneSetCollections function
In mssm-msf-2019/BiostatsALL:

Description Usage Arguments

This function runs a function that takes a list of gene set collections, a named phenotype vector (with names of the phenotype vector as the universe), a vector of hits (gene names only) and returns the results of hypergeometric and gene set enrichment analyses for all of the gene set collections (with multiple hypothesis testing corrections).

1
2
3

RunGeneSetCollection_MSF(listOfGeneSetCollections, geneList, hits,
  pAdjustMethod = "BH", pValueCutoff = 1, nPermutations = 1000,
  minGeneSetSize, fname = NULL)

`listOfGeneSetCollections`	a list of gene set collections (a 'gene set collection' is a list of gene sets). Even if only one collection is being tested, it must be entered as an element of a 1-element list, e.g. ListOfGeneSetCollections = list(YourOneGeneSetCollection). Naming the elements of listOfGeneSetCollections will result in these names being associated with the relevant data frames in the output (meaningful names are advised)
`geneList`	a numeric or integer vector of phenotypes in descending or ascending order with elements named by their EntrezIds (no duplicates nor NA values)
`hits`	a character vector of the EntrezIds of hits, as determined by the user
`pAdjustMethod`	a single character value specifying the p-value adjustment method to be used (see 'p.adjust' for details)
`pValueCutoff`	numeric value, p value of cut of
`nPermutations`	numeric value, number of permutations
`minGeneSetSize`	numeric value, minimun number of genes accepted
`fname`	character string, filename