bt.map: Apply a function to a column from B intervals that overlap A.

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Apply a function to a column from B intervals that overlap A.

Description

Apply a function to a column from B intervals that overlap A.

Usage

bt.map(
  a,
  b,
  c = NULL,
  o = NULL,
  delim = NULL,
  prec = NULL,
  s = NULL,
  S = NULL,
  f = NULL,
  F = NULL,
  r = NULL,
  e = NULL,
  split = NULL,
  g = NULL,
  nonamecheck = NULL,
  bed = NULL,
  header = NULL,
  nobuf = NULL,
  iobuf = NULL,
  output = NULL
)

Arguments

a	<bed/gff/vcf>
b	<bed/gff/vcf>
c	Specify columns from the B file to map onto intervals in A. Default: 5. Multiple columns can be specified in a comma-delimited list.
o	Specify the operation that should be applied to -c. Valid operations: sum, min, max, absmin, absmax, mean, median, mode, antimode stdev, sstdev collapse (i.e., print a delimited list (duplicates allowed)), distinct (i.e., print a delimited list (NO duplicates allowed)), distinct_sort_num (as distinct, sorted numerically, ascending), distinct_sort_num_desc (as distinct, sorted numerically, desscending), distinct_only (delimited list of only unique values), count count_distinct (i.e., a count of the unique values in the column), first (i.e., just the first value in the column), last (i.e., just the last value in the column), Default: sum Multiple operations can be specified in a comma-delimited list. If there is only column, but multiple operations, all operations will be applied on that column. Likewise, if there is only one operation, but multiple columns, that operation will be applied to all columns. Otherwise, the number of columns must match the the number of operations, and will be applied in respective order. E.g., "-c 5,4,6 -o sum,mean,count" will give the sum of column 5, the mean of column 4, and the count of column 6. The order of output columns will match the ordering given in the command.
delim	Specify a custom delimiter for the collapse operations. - Example: -delim "|" - Default: ",".
prec	Sets the decimal precision for output (Default: 5)
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".
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.