ELMER_RNA_Met_analysis: RNA and methylation analysis

In ProfessionalFarmer/loonR: Common function in bioinformatics analysis

RNA and methylation analysis

Description

RNA and methylation analysis

Usage

ELMER_RNA_Met_analysis(
  rna.df = NULL,
  met.df = NULL,
  group = NULL,
  genome = "hg19",
  met.platform = "450K",
  beta.dif = 0.2,
  dir.group1 = "hyper",
  specify.probes = NULL,
  TF.motif = FALSE,
  run.diff = TRUE
)

Arguments

rna.df	row name should be ensembl ID
met.df	row name should be probeID
group	normal 在前, cancer 在后
genome	hg19 or hg38
met.platform	450K or EPIC
beta.dif	Default 0.2. Beta difference
dir.group1	It can be "hypo" which means the probes are hypomethylated in group1; "hyper" which means the probes are hypermethylated in group1
specify.probes	Specify methylation probe instead of ELMER
TF.motif	Default FALSE. If perform TF and motif analysi
run.diff	If run methylation analysis

ProfessionalFarmer/loonR documentation built on Oct. 9, 2024, 9:56 p.m.