bt.closest: For each feature in A, finds the closest feature (upstream or...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

For each feature in A, finds the closest feature (upstream or downstream) in B.

Description

For each feature in A, finds the closest feature (upstream or downstream) in B.

Usage

bt.closest(
  a,
  b,
  d = NULL,
  D = NULL,
  io = NULL,
  iu = NULL,
  id = NULL,
  fu = NULL,
  fd = NULL,
  t = NULL,
  mdb = NULL,
  k = NULL,
  N = NULL,
  s = NULL,
  S = NULL,
  f = NULL,
  F = NULL,
  r = NULL,
  e = NULL,
  split = NULL,
  g = NULL,
  nonamecheck = NULL,
  names = NULL,
  filenames = NULL,
  sortout = NULL,
  bed = NULL,
  header = NULL,
  nobuf = NULL,
  iobuf = NULL,
  output = NULL
)

Arguments

a	<bed/gff/vcf>
b	<bed/gff/vcf>
d	In addition to the closest feature in B, report its distance to A as an extra column. - The reported distance for overlapping features will be 0.
D	Like -d, report the closest feature in B, and its distance to A as an extra column. Unlike -d, use negative distances to report upstream features. The options for defining which orientation is "upstream" are: - "ref" Report distance with respect to the reference genome. B features with a lower (start, stop) are upstream - "a" Report distance with respect to A. When A is on the - strand, "upstream" means B has a higher (start,stop). - "b" Report distance with respect to B. When B is on the - strand, "upstream" means A has a higher (start,stop).
io	Ignore features in B that overlap A. That is, we want close, yet not touching features only.
iu	Ignore features in B that are upstream of features in A. This option requires -D and follows its orientation rules for determining what is "upstream".
id	Ignore features in B that are downstream of features in A. This option requires -D and follows its orientation rules for determining what is "downstream".
fu	Choose first from features in B that are upstream of features in A. This option requires -D and follows its orientation rules for determining what is "upstream".
fd	Choose first from features in B that are downstream of features in A. This option requires -D and follows its orientation rules for determining what is "downstream".
t	How ties for closest feature are handled. This occurs when two features in B have exactly the same "closeness" with A. By default, all such features in B are reported. Here are all the options: - "all" Report all ties (default). - "first" Report the first tie that occurred in the B file. - "last" Report the last tie that occurred in the B file.
mdb	How multiple databases are resolved. - "each" Report closest records for each database (default). - "all" Report closest records among all databases.
k	Report the k closest hits. Default is 1. If tieMode = "all", - all ties will still be reported.
N	Require that the query and the closest hit have different names. For BED, the 4th column is compared.
s	Require same strandedness. That is, only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand.
S	Require different strandedness. That is, only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand.
f	Minimum overlap required as a fraction of A. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
F	Minimum overlap required as a fraction of B. - Default is 1E-9 (i.e., 1bp). - FLOAT (e.g. 0.50)
r	Require that the fraction overlap be reciprocal for A AND B. - In other words, if -f is 0.90 and -r is used, this requires that B overlap 90 percent of A and A _also_ overlaps 90 percent of B.
e	Require that the minimum fraction be satisfied for A OR B. - In other words, if -e is used with -f 0.90 and -F 0.10 this requires that either 90 percent of A is covered OR 10 percent of B is covered. Without -e, both fractions would have to be satisfied.
split	Treat "split" BAM or BED12 entries as distinct BED intervals.
g	Provide a genome file to enforce consistent chromosome sort order across input files. Only applies when used with -sorted option.
nonamecheck	For sorted data, don't throw an error if the file has different naming conventions for the same chromosome. ex. "chr1" vs "chr01".
names	When using multiple databases, provide an alias for each that will appear instead of a fileId when also printing the DB record.
filenames	When using multiple databases, show each complete filename instead of a fileId when also printing the DB record.
sortout	When using multiple databases, sort the output DB hits for each record.
bed	If using BAM input, write output as BED.
header	Print the header from the A file prior to results.
nobuf	Disable buffered output. Using this option will cause each line of output to be printed as it is generated, rather than saved in a buffer. This will make printing large output files noticeably slower, but can be useful in conjunction with other software tools and scripts that need to process one line of bedtools output at a time.
iobuf	Specify amount of memory to use for input buffer. Takes an integer argument. Optional suffixes K/M/G supported. Note: currently has no effect with compressed files.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.