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bedr (version 1.0.2)
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
1.0.2
License
GPL-2
Maintainer
Paul Boutros
Last Published
September 21st, 2015
Functions in bedr (1.0.2)
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bed2index
bed dataframe to index string
cluster.region
cluster intervals
flank.region
Get adjacent flanks from regions
bedr
Main bedtools wrapper function.
determine.input
Determine input format
get.chr.length
gets the length of each chromosome for a species/build
bedr.setup
Initialize some config settings for bedr
bedr.plot.region
Visualize regions or intervals
create.tmp.bed.file
output R objects as tmpfiles
bed2vcf
convert bed to vcf
bedr.sort.region
sort a region file
convert2bed
convert object to bed format
bedr.merge.region
merge i.e. collapse overlpaping regions
permute.region
permute a set of regions
jaccard
calculate the jaccard distance between sets of intervals
read.vcf
Read a vcf into R
bedr-package
A bedtools wrapper for working with genomic ranges in R
snm
sort a region file
bedr.subtract.region
subtracts features or ranges in object b from object a
is.merged.region
checks if region file is merged
strsplit2matrix
split a vector of strings into tabular data
process.input
process.input
is.sorted.region
checks if region file is sorted
size.region
Get region size
bedr.join.region
join two region objects using a left outer join
check.binary
checks if binary is in the path
vcf2bed
convert a vcf to a bed file
bedr.join.multiple.region
join multiple region objects
df2list
Data frame to list conversion
grow.region
Get adjacent flanks from regions
catv
outputs text if verbose flag is set
test.region.similarity
Compare sets of regions via jaccard and relative distance using permutation
get.example.regions
return a set of regions for the examples and unit testing
reldist
Calculate the relative distance between two sets of intervals
modifyList2
Interface to R's modifyList
get.fasta
Query fasta sequence
order.region
Gets the sort order of a region index similar to the order command
query.ucsc
read a ucsc table into R
is.valid.region
checks if region/index is valid
index2bed
convert a region index into a bed file dataframe
%in.region%
checks if regions in object a are found in object b
in.region
checks if regions in object a are found in object b
tabix
Main bedtools wrapper function.
is.valid.ref
verifies the reference sequence in a vcf
get.random.regions
generates a set of random regions
is.valid.seq
verifies that sequences are correct given coordinates and a reference
write.vcf
write a vcf object
download.datasets
Download some useful datasets
table2venn
Plot venn diagram