circClassification: circRNA classification using trancript information and the...

In tofazzal4720/FcircSEC: Full Length Circular RNA Sequence Extraction and Classification

Description

This function classifies circRNAs using the transcript information obtained from annotation file and the bedfile obtained from the circRNA prediction tools

Usage

circClassification(transcriptdata, bedfile, outfiletxt, outfilebed)

Arguments

transcriptdata	The transcript data (obtained from function transcriptExtract)
bedfile	The bed file (obtained from the circRNA prediction tools) having four columns chromosome, circRNA start, circRNA end position and circRNA strand
outfiletxt	The output file with the detailed information of circRNA classification
outfilebed	The output file with chromosome, start and end position of each circRNAs

Value

The detailed information of circRNA classification will be written in outfiletxt and only chromosome, start and end position of each circRNAs will be written in outfilebed

Examples

#Loading and example transcript data and write to a file
#Here temporary directory is created as input-output
#directory. Please provide you own directory instead.
out_dir<-tempdir()
t_data<-data("transcript_data") 
t_data<-transcript_data
write.table(t_data, file.path(out_dir,"transcript_data.txt"), row.names=FALSE)

#Loading an example bedfile obtained form the circRNA prediction tool and write to a file
b_file<-data("output_CIRI")
b_file<-output_CIRI
write.table(b_file, file.path(out_dir,"output_CIRI.bed"), col.names=FALSE, row.names=FALSE)

#Classification of circRNAs. Here, the output will be written in two files 
#circRNA_class.txt and circRNA_class.bed in out_dir directory
circClassification (file.path(out_dir,"transcript_data.txt"), 
   file.path(out_dir,"output_CIRI.bed"), file.path(out_dir, "circRNA_class.txt"), 
   file.path(out_dir, "circRNA_class.bed"))

tofazzal4720/FcircSEC documentation built on Jan. 26, 2020, 7:50 a.m.