FastCeRNA_edge2: a simple method for ceRNA network edge/node selection

In shijianasdf/BasicBioinformaticsAnalysisFromZhongShan: Launch Usual Clinical tool for Kind Yield

Description

a simple method for ceRNA network edge/node selection

Usage

FastCeRNA_edge2(object, lncRNA.col = "lncRNAs", pcRNA.col = "Genes",
  miRNA.col = "miRNAs", pmcor = "pmcor", pmcor.Pvalue = "corPValue",
  lmcor = "lmcor", plcor = "plcor", cutoff = list(pl = 0.5, lm = 0.2,
  pm = 0.2), filter = T, verbose = T)

Arguments

object	the result of FastCeRNA
lncRNA.col	colnames of lncRNA
pcRNA.col	colnames of protein-coding RNA,
miRNA.col	colnames of miRNA
pmcor	the col of protein-coding and miRNA correlation
pmcor.Pvalue	the p value of pmcor
lmcor	the col of lncRNA and miRNA correlation
plcor	the col of protein-coding and miRNA correlation
cutoff	the cutoff of correlation.Default is list(pl=0.5,lm=0.2,pm=0.2)
filter	whether to do filter
verbose	whether do verbose report

Details

FastCeRNA_edge2 select ceRNA network:positive lnc-miRNA correaltion;miR negative.

Value

a data frame

Author(s)

Weibin Huang<[e-mail]>

Examples

## This is a simulative process and available only with CORRECT VARIABLES
load("E:/iProjects/LM_WGCNA/data/LM_WGCNA_02C/rda/lm_ceRNA.rda")
df <- FastCeRNA_edge2(object)

## other parameters
colnames(lm_ceRNA)
object = lm_ceRNA
lncRNA.col = "lncRNAs"
pcRNA.col = "Genes"
miRNA.col = "miRNAs"
pmcor = "pmcor"
lmcor="lmcor"
plcor = "plcor"
filter = T
verbose = T

shijianasdf/BasicBioinformaticsAnalysisFromZhongShan documentation built on Jan. 3, 2020, 10:08 p.m.