moonlight {MoonlightR} | R Documentation |
moonlight is a tool for identification of cancer driver genes. This function wraps the different steps of the complete analysis workflow. Providing different solutions:
MoonlighR::FEA
MoonlighR::URA
MoonlighR::PIA
moonlight(cancerType = "panCancer", dataType = "Gene expression", directory = "GDCdata", BPname = NULL, cor.cut = 0.6, qnt.cut = 0.25, Genelist = NULL, fdr.cut = 0.01, logFC.cut = 1, corThreshold = 0.6, kNearest = 3, nGenesPerm = 10, DiffGenes = FALSE, nBoot = 100, nTF = NULL, nSample = NULL, thres.role = 0, stage = NULL, subtype = 0, samples = NULL)
cancerType |
select cancer type for which analysis should be run. panCancer for all available cancer types in TCGA. Defaults to panCancer |
dataType |
dataType |
directory |
directory |
BPname |
biological processes to use, if NULL: all processes will be used in analysis, RF for candidate; if not NULL the candidates for these processes will be determined (no learning) |
cor.cut |
cor.cut Threshold |
qnt.cut |
qnt.cut Threshold |
Genelist |
Genelist |
fdr.cut |
fdr.cut Threshold |
logFC.cut |
logFC.cut Threshold |
corThreshold |
corThreshold |
kNearest |
kNearest |
nGenesPerm |
nGenesPerm |
DiffGenes |
DiffGenes |
nBoot |
nBoot |
nTF |
nTF |
nSample |
nSample |
thres.role |
thres.role |
stage |
stage |
subtype |
subtype |
samples |
samples |
table with cancer driver genes TSG and OCG.
dataDEGs <- DPA(dataFilt = dataFilt, dataType = "Gene expression") # to change with moonlight