Main wrapper for iEDGE, assumes input data is constructed by construct_iEDGE

Main wrapper for iEDGE, assumes input data is constructed by construct_iEDGE

run_iEDGE(dat, header, outdir, gs.file = NA, gepid = "SYMBOL",
  cnid = "Unique.Name", cndesc = "Descriptor",
  cndir = "alteration_direction", fdr.cis.cutoff = 0.25,
  fdr.trans.cutoff = 0.05, fc.cis = NA, fc.trans = NA,
  min.drawsize = 3, onesided.cis = TRUE, onesided.trans = FALSE,
  uptest = "Amplification", downtest = "Deletion", min.group = 2,
  prune.col = "pvalue", prune.thres = 0.05, hyperthres = 0.25,
  cis.boxplot = TRUE, trans.boxplot = TRUE, enrichment = TRUE,
  bipartite = TRUE, html = TRUE, jsdir = NA, numcores = NA,
  cache = list(DE = NULL, DE.enrich = NULL, prunning = NULL,
  pruning.enrich = NULL, ui = NULL), includeheatmap = TRUE)

Arguments

dat	the input iEDGE object, see construct_iEDGE for specification
header	header string for result file names
outdir	output directory
gs.file	default = NA, vector of characters giving full path of gmt files for enrichment analysis
gepid	default = "SYMBOL", colname in fData(dat$gep) indicating unique gene ids to display
cnid	default = "Unique.Name", colname in fData(dat$cn) indicating unique alterations to display
cndesc	default = "Descriptor", column in fData(dat$cn), can be NA if not available
cndir	default = "alteration_direction", column in fData(dat$cn) indicating directions of one sided differential expression, use NA if onesided.cis = FALSE and onesided.trans = FALSE
fdr.cis.cutoff	default = 0.25, fdr cis cutoff
fdr.trans.cutoff	default = 0.05, fdr trans cutoff
fc.cis	default = NA, fold change cutoff cis
fc.trans	default = NA, fold change cutoff trans
min.drawsize	default = 3, min drawsize for geneset enrichment
onesided.cis	default = TRUE, one sided cis differential expression
onesided.trans	default = FALSE, one sided trans differential expression
uptest	default = "Amplification", alterations for which upregulation in alteration is desired, value must be on fData(dat$cn)[, cndir], must specify if onesided.cis =TRUE
downtest	= "Deletion", alterations for which downregulation in alteration is desired
min.group	default = 2, mininum sample size in each group
prune.col	default = "pvalue", column name to indicate significance of sobel test
prune.thres	default = 0.05, significance cutoff of sobel test
hyperthres	default = 0.25, threshold for hyperEnrichment (fdr cutoff)
cis.boxplot	default = TRUE, display boxplot for cis genes
trans.boxplot	default = TRUE, display boxplot for trans genes
bipartite	default = TRUE, do bipartite graph/pruning
html	default = TRUE, do html report
jsdir	default = NA, default directory of iEDGE js files
numcores	default = NA (non-parallel), if specified uses mclapply with specified mc.cores
cache	default = list(DE = NULL, prunning = NULL, ui = NULL), optional, cached result of previous run_iEDGE
includeheatmap	= TRUE, optional, include heatmap for pathway enrichment in UI, must be enrichment=TRUE for this to work
enrich.heatmap	= TRUE, display heatmap for pathway enrichment results