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