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bedr (version 1.0.1)
Genomic Region Processing using Tools Such as Bedtools, Bedops and Tabix
Description
Genomic region processing using tools such as bedtools, bedops and tabix.
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Install
install.packages('bedr')
Monthly Downloads
721
Version
1.0.1
License
GPL-2
Maintainer
Paul Boutros
Last Published
September 5th, 2015
Functions in bedr (1.0.1)
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tabix
Main bedtools wrapper function.
%in.region%
checks if regions in object a are found in object b
determine.input
Determine input format
download.datasets
Download some useful datasets
cluster.region
cluster intervals
is.sorted.region
checks if region file is sorted
bedr.merge.region
merge i.e. collapse overlpaping regions
convert2bed
convert object to bed format
write.vcf
write a vcf object
get.random.regions
generates a set of random regions
table2venn
Plot venn diagram
bedr.join.multiple.region
join multiple region objects
get.chr.length
gets the length of each chromosome for a species/build
permute.region
permute a set of regions
create.tmp.bed.file
output R objects as tmpfiles
flank.region
Get adjacent flanks from regions
jaccard
calculate the jaccard distance between sets of intervals
bedr.plot.region
Visualize regions or intervals
catv
outputs text if verbose flag is set
bedr.setup
Initialize some config settings for bedr
modifyList2
Interface to R's modifyList
check.binary
checks if binary is in the path
order.region
Gets the sort order of a region index similar to the order command
in.region
checks if regions in object a are found in object b
is.valid.region
checks if region/index is valid
bed2index
bed dataframe to index string
bedr.subtract.region
subtracts features or ranges in object b from object a
query.ucsc
read a ucsc table into R
get.fasta
Query fasta sequence
bed2vcf
convert bed to vcf
is.valid.ref
verifies the reference sequence in a vcf
bedr-package
A bedtools wrapper for working with genomic ranges in R
process.input
process.input
grow.region
Get adjacent flanks from regions
index2bed
convert a region index into a bed file dataframe
bedr
Main bedtools wrapper function.
test.region.similarity
Compare sets of regions via jaccard and relative distance using permutation
bedr.join.region
join two region objects using a left outer join
vcf2bed
convert a vcf to a bed file
size.region
Get region size
is.merged.region
checks if region file is merged
bedr.sort.region
sort a region file
read.vcf
Read a vcf into R
strsplit2matrix
split a vector of strings into tabular data
get.example.regions
return a set of regions for the examples and unit testing
is.valid.seq
verifies that sequences are correct given coordinates and a reference
reldist
Calculate the relative distance between two sets of intervals
snm
sort a region file
df2list
Data frame to list conversion