Summarize DNA sequences over the specified ranges.
bedtools_nuc(cmd = "--help") R_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = FALSE) do_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = FALSE)
String of bedtools command line arguments, as they would be entered at the shell. There are a few incompatibilities between the docopt parser and the bedtools style. See argument parsing.
Path to a FASTA file, or an XStringSet.
Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or
a ranged data structure, such as a GRanges, as the query. Use
Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented.
Optional sequence pattern to count in each subsequence.
Use the full FASTA header as the names. By default, use just the first word.
As with all commands, there are three interfaces to the
Parses the bedtools command line and compiles it to the equivalent R code.
Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
Evaluates the result of
R_bedtools_nuc. Recommended only for
demonstration and testing. It is best to integrate the compiled
code into an R script, after studying it.
Computes AT/GC percentage and counts each type of base. Relies on
Biostrings utilities like
alphabetFrequency. The counting of
pattern occurrences uses
A language object containing the compiled R code, evaluating to a
DataFrame with summary statistics including the AC and GT
percentage, and the counts of each type of base. Also includes the
pattern, if specified.
letterFrequency for summarizing sequences, matchPattern for pattern matching.
## Not run: setwd(system.file("unitTests", "data", "nuc", package="HelloRanges")) ## End(Not run) ## default behavior, note the two dashes in '--fi' bedtools_nuc("--fi test.fasta -bed a.bed") ## with pattern counting bedtools_nuc("--fi test.fasta -bed a.bed -pattern ATA")
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