Genomic Region Processing using Tools Such as 'BEDTools',
'BEDOPS' and 'Tabix'
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Documentation for package ‘bedr’ version 1.1.3
Help Pages
| %in.region% | checks if regions in object a are found in object b |
| adjust.coordinates | adjust coordinates for a BEDPE file |
| 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.bedpe.id | get BEDPE ID from VCF ID |
| 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 |
| get.strand | get BEDPE ID from VCF ID |
| 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 |
| vcf2bedpe | convert a vcf to a bedpe file |
| write.vcf | write a vcf object |