Description Usage Arguments Value Examples
View source: R/get_fasta_utils.R
Extracts promoter sequences from input bed/gff file
1 2 3 4 5 6 7 8 | get_promoter_from_feature(
feature_file,
fasta_file,
write_outputfasta = FALSE,
write_promoterbed = FALSE,
upstream_bp = 500,
downstream_bp = 1
)
|
feature_file |
Either a path or a connection to either
a 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 list 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. |
write_outputfasta |
Logical, to return promoter sequences as a output multi-fasta file, Default: FALSE |
write_promoterbed |
Logical, to return promoter regions as a output bed file, Default: FALSE |
upstream_bp |
numeric, base pairs window upstream of start coordinate, Default: 500 |
downstream_bp |
numeric, base pairs window downstream of start coordinate, Default: 1 |
sequences of promoters and bed file of the promoter region
1 2 3 4 5 6 7 8 9 | ## Not run:
feature_file_in <- system.file("exdata","Sc_ref_genes.gff", package = "fastaR")
ref_fasta <- system.file("exdata", "Sc_ref_genome.fasta", package = "fastaR")
fastaR::get_promoter_from_feature(feature_file=feature_file_in, fasta_file=ref_fasta,
write_outputfasta= FALSE, write_promoterbed= FALSE, upstream_bp= 1000, downstream_bp= 100)
## End(Not run)
|
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