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bedr (version 1.0.0)
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
1.0.0
License
GPL-2
Maintainer
Paul Boutros
Last Published
September 4th, 2015
Functions in bedr (1.0.0)
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bedr
Main bedtools wrapper function.
catv
outputs text if verbose flag is set
bedr-package
A bedtools wrapper for working with genomic ranges in R
bedr.sort.region
sort a region file
get.chr.length
gets the length of each chromosome for a species/build
read.vcf
Read a vcf into R
is.valid.ref
verifies the reference sequence in a vcf
bedr.merge.region
merge i.e. collapse overlpaping regions
cluster.region
cluster intervals
reldist
Calculate the relative distance between two sets of intervals
create.tmp.bed.file
output R objects as tmpfiles
bedr.setup
Initialize some config settings for bedr
query.ucsc
read a ucsc table into R
get.example.regions
return a set of regions for the examples and unit testing
bedr.subtract.region
subtracts features or ranges in object b from object a
convert2bed
convert object to bed format
modifyList2
Interface to R's modifyList
%in.region%
checks if regions in object a are found in object b
determine.input
Determine input format
grow.region
Get adjacent flanks from regions
check.binary
checks if binary is in the path
process.input
process.input
df2list
Data frame to list conversion
is.sorted.region
checks if region file is sorted
snm
sort a region file
test.region.similarity
Compare sets of regions via jaccard and relative distance using permutation
get.fasta
Query fasta sequence
get.random.regions
generates a set of random regions
is.valid.region
checks if region/index is valid
strsplit2matrix
split a vector of strings into tabular data
is.valid.seq
verifies that sequences are correct given coordinates and a reference
is.merged.region
checks if region file is merged
write.vcf
write a vcf object
tabix
Main bedtools wrapper function.
flank.region
Get adjacent flanks from regions
bedr.plot.region
Visualize regions or intervals
jaccard
calculate the jaccard distance between sets of intervals
in.region
checks if regions in object a are found in object b
order.region
Gets the sort order of a region index similar to the order command
index2bed
convert a region index into a bed file dataframe
table2venn
Plot venn diagram
vcf2bed
convert a vcf to a bed file
bed2vcf
convert bed to vcf
bedr.join.multiple.region
join multiple region objects
bedr.join.region
join two region objects using a left outer join
bed2index
bed dataframe to index string
download.datasets
Download some useful datasets
permute.region
permute a set of regions
size.region
Get region size