bedr-package |
A bedtools wrapper for working with genomic ranges in R |
%in.region% |
checks if regions in object a are found in object b |
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.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 |
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 |
write.vcf |
write a vcf object |