moonlight: moonlight pipeline

View source: R/moonlight.R

moonlightR Documentation

moonlight pipeline

Description

moonlight is a tool for identification of cancer driver genes. This function wraps the different steps of the complete analysis workflow. Providing different solutions:

  1. MoonlighR::FEA

  2. MoonlighR::URA

  3. MoonlighR::PIA

Usage

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
)

Arguments

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

Value

table with cancer driver genes TSG and OCG.

Examples

dataDEGs <- DPA(dataFilt = dataFilt, dataType = "Gene expression")
# to change with moonlight

ELELAB/MoonlightR documentation built on May 16, 2024, 4:21 p.m.