ceRNANet: Get ceRNA network from starBase 3.0 by giving miRNAs symbol

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

Description

Get ceRNA network by giving miRNAs symbol

Usage

ceRNANet(assembly = "hg19", geneType = "lncRNA", ceRNA = "HOTAIR",
  miRNAnum = 2, family = "all", pval = 0.01, fdr = 0.01,
  pancancerNum = 0, verbose = T)

Arguments

assembly	genome reference of a species.Default is homo spacies("hg19").See starbase
geneType	"mRNA","lncRNA","pseudogene","sncRNA".See starbase
ceRNA	If you set a lncRNA as ceRNA,you should set geneType="lncRNA"
miRNAnum	Default is 2.See starbase
family	miRNA family names.See starbase
pval	Default is 0.01.See starbase
fdr	Default is 0.01.See starbase
pancancerNum	Default is 0.See starbase
verbose	whether to show verbose report

Value

a data frame with ceRNA interaction information

Author(s)

Weibin Huang<[e-mail]>

See Also

starbasehttp://starbase.sysu.edu.cn/

Examples

## Get specified miRNA based ceRNA network
ceRNA = c("ENSG00000228630","ENSG00000228630","FKDKEK","FKDKEK")
family = "all"
# Or:
ceRNA = c("ENSG00000228630","ENSG00000228630","FKDKEK","FKDKEK")
family = "ABCKD" # Here,family parameter would be corrected to "all"

## Get specified miRNA based ceRNA network
ceRNA <- "all"
family <-  c("miR-1252-5p","miR-200bc-3p/429")

## Get specified lncRNA-miRNA based ceRNA network
ceRNA = c("ENSG00000228630")
family <-  c("miR-1252-5p","miR-200bc-3p/429")

## Get all lncRNA based ceRNA network
ceRNA <- "all"
family <-  "all"
net_ceRNA <- ceRNANet(assembly = "hg19",
                      geneType="lncRNA",
                      ceRNA,
                      miRNAnum=2,
                      family,
                      pval=0.01,
                      fdr=0.01,
                      pancancerNum=0,
                      verbose = T)

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