Main wrapper for iEDGE, assumes input data is constructed by construct_iEDGE
1 2 3 4 5 6 7 8 9 10 11 | 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)
|
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 |
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