CreateOutputsMA: A function that creates a table with the results of limma...
In mssm-msf-2019/BiostatsALL:

a function that takes ebfit as input and create a table with DEG genes

CreateOutputsMA(ebfit, AnnPkg, Decision = NULL,
  coefs = c(1:ncol(ebfit$coef)), adjmeth = "fdr", mcut = 2, fname = "",
  pcut = 0.05, html.genetable = TRUE, exprset = NULL, annotTable = NULL,
  which.annot = c("ENTREZID", "SYMBOL", "GENENAME", "OMIM", "CHRLOC"),
  which.annot.unique = c("ENTREZID", "SYMBOL", "OMIM", "CHRLOC"),
  pPath = 0.1, pGO = pPath, nPath = 2, pPFAM = pPath)

`ebfit`	has estimates of contrasts
`AnnPkg`	package used to annotate data (example: hgu133plus2.db)
`Decision`	is the matrix with -1 0 1 indicating gene regulation
`coefs`	is a matrix with the coefficients of the models
`adjmeth`	is the criterion for adjusting pvalues
`mcut`	is the cutoff for log2 fold-changes
`fname`	is the output filename
`pcut`	is the threshold for pvalues
`html.genetable`	logical parameter to create html table with results
`exprset`	is the matrix with gene expressions
`annotTable`	is a table with annotation about the gens
`which.annot`	is a selection of which annotations should be used
`which.annot.unique`	is a selection of which annotations should be unique
`pPath`	is the pvalue cutoff for pathway analysis
`pGO`	is the pvalue cutoff for annotation in Gene Ontology Database
`nPath`	?????
`pPFAM`	is the cutoff for annotation in Protein Family DataBase

CreateOutputsMA(ebfit, AnnPkg, Decision=NULL, coefs=c(1:ncol(ebfit$coef)), adjmeth='fdr', mcut=2,
fname="", pcut=0.05, html.genetable =TRUE, exprset=NULL, annotTable=NULL,
which.annot= c("ENTREZID","SYMBOL","GENENAME","OMIM","CHRLOC"),
which.annot.unique=c("ENTREZID","SYMBOL","OMIM","CHRLOC"),
pPath=0.1, pGO=pPath, nPath=2, pPFAM=pPath)