Man pages for bedr
Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

bed2indexbed dataframe to index string
bed2vcfconvert bed to vcf
bedrMain bedtools wrapper function.
bedr.join.multiple.regionjoin multiple region objects
bedr.join.regionjoin two region objects using a left outer join
bedr.merge.regionmerge i.e. collapse overlpaping regions
bedR-packageA bedtools wrapper for working with genomic ranges in R
bedr.plot.regionVisualize regions or intervals
bedr.setupInitialize some config settings for bedr
bedr.snm.regionsort a region file
bedr.sort.regionsort a region file
bedr.subtract.regionsubtracts features or ranges in object b from object a
catvoutputs text if verbose flag is set
check.binarychecks if binary is in the path
cluster.regioncluster intervals
convert2bedconvert object to bed format
create.tmp.bed.fileoutput R objects as tmpfiles
determine.inputDetermine input format
df2listData frame to list conversion
download.datasetsDownload some useful datasets
flank.regionGet adjacent flanks from regions
get.chr.lengthgets the length of each chromosome for a species/build
get.example.regionsreturn a set of regions for the examples and unit testing
get.fastaQuery fasta sequence
get.random.regionsgenerates a set of random regions
grow.regionGet adjacent flanks from regions
index2bedconvert a region index into a bed file dataframe
in.regionchecks if regions in object a are found in object b
in.region2checks if regions in object a are found in object b
is.merged.regionchecks if region file is merged
is.sorted.regionchecks if region file is sorted
is.valid.refverifies the reference sequence in a vcf
is.valid.regionchecks if region/index is valid
is.valid.seqverifies that sequences are correct given coordinates and a...
jaccardcalculate the jaccard distance between sets of intervals
modifyList2Interface to R's modifyList
order.regionGets the sort order of a region index similar to the order...
permute.regionpermute a set of regions
query.ucscread a ucsc table into R
read.vcfRead a vcf into R
reldistCalculate the relative distance between two sets of intervals
size.regionGet region size
strsplit2matrixsplit a vector of strings into tabular data
tabixMain bedtools wrapper function.
table2vennPlot venn diagram
test.region.similarityCompare sets of regions via jaccard and relative distance...
vcf2bedconvert a vcf to a bed file
write.vcfwrite a vcf object
bedr documentation built on May 2, 2019, 11:36 a.m.