Description Usage Arguments Value Author(s) See Also Examples
Get ceRNA network by giving miRNAs symbol
1 2 3 |
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 |
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 |
a data frame with ceRNA interaction information
Weibin Huang<654751191@qq.com>
starbase
http://starbase.sysu.edu.cn/
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 | ## 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)
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