Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

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Documentation for package ‘bedr’ version 1.0.7

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bedr-package A bedtools wrapper for working with genomic ranges in R
%in.region% checks if regions in object a are found in object b
bed2index bed dataframe to index string
bed2vcf convert bed to vcf
bedr Main bedtools wrapper function.
bedr.join.multiple.region join multiple region objects
bedr.join.region join two region objects using a left outer join
bedr.merge.region merge i.e. collapse overlpaping regions
bedr.plot.region Visualize regions or intervals
bedr.setup Initialize some config settings for bedr
bedr.snm.region sort a region file
bedr.sort.region sort a region file
bedr.subtract.region subtracts features or ranges in object b from object a
catv outputs text if verbose flag is set
check.binary checks if binary is in the path
cluster.region cluster intervals
convert2bed convert object to bed format
create.tmp.bed.file output R objects as tmpfiles
determine.input Determine input format
df2list Data frame to list conversion
download.datasets Download some useful datasets
flank.region Get adjacent flanks from regions
get.chr.length gets the length of each chromosome for a species/build
get.example.regions return a set of regions for the examples and unit testing
get.fasta Query fasta sequence
get.random.regions generates a set of random regions
grow.region Get adjacent flanks from regions
in.region checks if regions in object a are found in object b
index2bed convert a region index into a bed file dataframe
is.merged.region checks if region file is merged
is.sorted.region checks if region file is sorted
is.valid.ref verifies the reference sequence in a vcf
is.valid.region checks if region/index is valid
is.valid.seq verifies that sequences are correct given coordinates and a reference
jaccard calculate the jaccard distance between sets of intervals
modifyList2 Interface to R's modifyList
order.region Gets the sort order of a region index similar to the order command
permute.region permute a set of regions
process.input process.input
query.ucsc read a ucsc table into R
read.vcf Read a vcf into R
reldist Calculate the relative distance between two sets of intervals
size.region Get region size
strsplit2matrix split a vector of strings into tabular data
tabix Main bedtools wrapper function.
table2venn Plot venn diagram
test.region.similarity Compare sets of regions via jaccard and relative distance using permutation
vcf2bed convert a vcf to a bed file
write.vcf write a vcf object