Description Usage Arguments Value Examples
This function can extract the sequences from the reference genome for the given intervals (start, end) of chromosomes
1 | get.fasta(ref_genome, circ_class_bed, out_filename)
|
ref_genome |
The reference genome |
circ_class_bed |
The bed file having chromosome, start and end position of each circRNAs (obtained from function |
out_filename |
The name of the output file |
The fasta file of the sequences extracted from the reference genome for the given intervals will be written in the output file 'out_filename'
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | #Loading an example reference genome and write to a file
#Here temporary directory is created as input-output
#directory. Please provide you own directory instead.
out_dir<-tempdir()
ref_genom<-data("chr1")
ref_genom<-chr1
df.fasta=dataframe2fas(ref_genom, file.path(out_dir, "ref_genome.fasta"))
#Loading an example circRNA classification bed file and write to a file
circ_class_bed<-data("circRNA_classb")
circ_class_bed<-circRNA_classb
write.table(circ_class_bed, file.path(out_dir, "circ_class.bed"),
col.names=FALSE, row.names=FALSE)
#Getting genomic sequences of circRNAs. The output will be
#generated in file circRNA_genomic_seq.fasta in out_dir directory
get.fasta(file.path(out_dir, "ref_genome.fasta"),
file.path(out_dir, "circ_class.bed"),
file.path(out_dir, "circRNA_genomic_seq.fasta"))
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