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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/BI_ceRNANet.R

Description

Get ceRNA network by giving miRNAs symbol

Usage

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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<[email protected]>

See Also

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

Examples

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## 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.