circrnaAnnotations.Rd
This function executes the docker container ciri2 in the annotation mode to overlap a list of circRNAs with the annotations from circBase, CSCD, ExoRBase, Circ2Disease, CircFunBase, and TSCD
circrnaAnnotations( group = c("sudo", "docker"), scratch.folder, ciri.file, annotation.sources = c("circbase", "tscd", "cscd", "exorbase", "circ2disease", "circfunbase"), assembly = c("hg18", "hg19", "hg38", "mm9", "mm10") )
group, | a character string. Two options: |
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scratch.folder, | a character string indicating the scratch folder where docker container will be mounted |
ciri.file, | a list of circRNAs derived from a circRNAs prediction analysis |
annotation.sources, | a vector of character strings indicating the circRNA databases to analyse. Compatible databases id: circbase, cscd, exorbase, circ2disease, circfunbase, tscd. |
assembly, | a character string indicating the reference genome assembly. The function currently work with the hg18, hg19, and hg38, mm9, and mm10 genome assemblies. |
The annotations of a list of circRNAs from different databases
if (FALSE) { # Retrieve the example data system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip") system("unzip master.zip") # Run the circAnnotations function circAnnotations(group = "docker", scratch.folder="/data/scratch", ciri.file=paste(getwd(),"/circhunter-master/CircHunter/data/circRNA_CRC.bed", sep=""), assembly="hg19") circAnnotations() }