moonlight | 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
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