Description Usage Arguments Value Examples
View source: R/get_fasta_utils.R
Extracts sequences from a fasta file for each of the intervals defined in a BED file
1 | get_fasta_from_bed(bedFile, fasta_file, write_output = FALSE)
|
bedFile |
Either a path or a connection to the bed
file, file format should be standard UCSC bed format with column:
|
fasta_file |
Either a path or a connection to reference multi-fasta file, from which subset of sequences for given input feature is to be retrieved. In the sequence header: only string before first space and/or first colon (:) will be considered for further processes. **Important consideration when header have long names. |
outfile |
Logical, to return output sequences as a output multi-fasta file or not, default: FALSE |
sequences in given bed region
1 2 3 4 5 6 7 8 | ## Not run:
bed_file_in <- system.file("exdata","Sc_ref_genes.bed", package = "fastaR")
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")
fastaR::get_fasta_from_bed(bedFile=bed_file_in, fasta_file=ref_fasta, write_output=FALSE)
## End(Not run)
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