Bedtools Wrapper

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Documentation for package ‘bedtoolsr’ version 2.30.0-2

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bt.annotate Annotates the depth & breadth of coverage of features from mult. files on the intervals in -i.
bt.bamtobed Converts BAM alignments to BED6 or BEDPE format.
bt.bamtofastq Convert BAM alignments to FASTQ files.
bt.bed12tobed6 Splits BED12 features into discrete BED6 features.
bt.bedpetobam Converts feature records to BAM format.
bt.bedtobam Converts feature records to BAM format.
bt.closest For each feature in A, finds the closest feature (upstream or downstream) in B.
bt.cluster Clusters overlapping/nearby BED/GFF/VCF intervals.
bt.complement Returns the base pair complement of a feature file.
bt.coverage Returns the depth and breadth of coverage of features from B on the intervals in A.
bt.expand Replicate lines in a file based on columns of comma-separated values.
bt.fisher Calculate Fisher statistic b/w two feature files.
bt.flank Creates flanking interval(s) for each BED/GFF/VCF feature.
bt.genomecov Compute the coverage of a feature file among a genome.
bt.getfasta Extract DNA sequences from a fasta file based on feature coordinates.
bt.groupby Summarizes a dataset column based upon common column groupings. Akin to the SQL "group by" command.
bt.igv Creates a batch script to create IGV images at each interval defined in a BED/GFF/VCF file.
bt.intersect Report overlaps between two feature files.
bt.jaccard Calculate Jaccard statistic b/w two feature files. Jaccard is the length of the intersection over the union. Values range from 0 (no intersection) to 1 (self intersection).
bt.links Creates HTML links to an UCSC Genome Browser from a feature file.
bt.makewindows Makes adjacent or sliding windows across a genome or BED file.
bt.map Apply a function to a column from B intervals that overlap A.
bt.maskfasta Mask a fasta file based on feature coordinates.
bt.merge Merges overlapping BED/GFF/VCF entries into a single interval.
bt.multicov Counts sequence coverage for multiple bams at specific loci.
bt.multiinter Identifies common intervals among multiple BED/GFF/VCF files.
bt.nuc Profiles the nucleotide content of intervals in a fasta file.
bt.overlap Computes the amount of overlap (positive values) or distance (negative values) between genome features and reports the result at the end of the same line.
bt.pairtobed Report overlaps between a BEDPE file and a BED/GFF/VCF file.
bt.pairtopair Report overlaps between two paired-end BED files (BEDPE).
bt.random Generate random intervals among a genome.
bt.reldist Calculate the relative distance distribution b/w two feature files.
bt.sample Take sample of input file(s) using reservoir sampling algorithm.
bt.shift Shift each feature by requested number of base pairs.
bt.shuffle Randomly permute the locations of a feature file among a genome.
bt.slop Add requested base pairs of "slop" to each feature.
bt.sort Sorts a feature file in various and useful ways.
bt.spacing Report (last col.) the gap lengths between intervals in a file.
bt.split Split a Bed file.
bt.subtract Removes the portion(s) of an interval that is overlapped by another feature(s).
bt.summary Report summary statistics of the intervals in a file
bt.tag Annotates a BAM file based on overlaps with multiple BED/GFF/VCF files on the intervals in -i.
bt.unionbedg Combines multiple BedGraph files into a single file, allowing coverage comparisons between them.
bt.window Examines a "window" around each feature in A and reports all features in B that overlap the window. For each overlap the entire entry in A and B are reported.
createOptions Creates options based on user input
deleteTempFiles Deletes temp files
establishPaths Determines if arguments are paths or R objects. Makes temp files when neccesary. Makes a list of files to use in bedtools call. Makes a list of temp files to delete at end of function.