bedr: Main bedtools wrapper function.

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

Description

Main bedtools wrapper function.

Usage

bedr(engine = "bedtools", 
	params = NULL,
	input = list(),
	method = NULL,
	tmpDir = NULL,
	deleteTmpDir = TRUE,
	outputDir = NULL,
	outputFile = NULL,
	check.chr = TRUE,
	check.zero.based = TRUE,
	check.valid = TRUE,
	check.sort = TRUE,
	check.merge = TRUE,
	verbose = TRUE
	);

Arguments

engine	What analytical engine to use i.e. bedtools, bedops, tabix, unix
params	A string that includes all the extra parameters and arguments to the bedtools commmand. For example if you wanted to do a left outer join you would specificy method as intersect and use params = c("-loj -header"). If you leave input and method as defaults then this is this string represents the full command.
input	A list of input items to be used by bedtools. Each item should be named by its parameter name in bedtools for example input = list(a=xxx, b=yyy, i=zzz). Items can be R objects or external files. R objects need to be in bed format i.e. have chr, start, stop as the first three columns, or, have an position index as the first column or rowname i.e. chr1:100-1000.
method	What bedtools method. This can be intersect, sort, merge etc. See bedtools documentation for specifcis.
tmpDir	The directory to be used for writing files
deleteTmpDir	Should tmp files be deleted. helpful for diagnostics.
outputDir	The output directory. Only used if outputFile is specified. It defaults to the current working directory.
outputFile	The name of the output file. If this is specified the output will be sent to a file not an R object
check.chr	check for chr prefix
check.zero.based	check for zero based coordinates
check.valid	do all region integrity checks
check.sort	check if region is sorted
check.merge	check if region is merged
verbose	Should messages be printed to screen.

Value

The output of command with some parsing to keep it consistent with the input.

Author(s)

Daryl Waggott

See Also

iranges

Examples

if (check.binary("bedtools")) {
set.seed(666)

index <- get.example.regions();
a <- index[[1]];
b <- index[[2]];

### check
is.a.valid  <- is.valid.region(a);
is.b.valid  <- is.valid.region(b);
a <- a[is.a.valid];
b <- b[is.b.valid];

### sort
is.sorted <- is.sorted.region(a);
a.sort1 <- bedr(engine = "bedtools", input = list(i = a), method = "sort", params = "");
b.sort1 <- bedr(engine = "bedtools", input = list(i = b), method = "sort", params = "");
a.sort2 <- bedr(engine = "bedops",   input = list(i = a), method = "sort", params = "");

a.sort3 <- bedr.sort.region(a);
a.sort4 <- bedr.sort.region(a, engine = "unix", method = "natural");
a.sort5 <- bedr.sort.region(a, engine = "R", method = "natural");

### merge
is.merged <- is.merged.region(a.sort1);
a.merge1 <- bedr(engine = "bedtools", input = list(i = a.sort1), method = "merge", params = "");
b.merge1 <- bedr(engine = "bedtools", input = list(i = b.sort1), method = "merge", params = "");
a.merge2 <- bedr(engine = "bedops",   input = list(i = a.sort1), method = "merge", params = "");
# a.merge3 <- bedr.merge.region(a); this will throw an error b/c region is not sorted

### subtract
a.sub1 <- bedr(input = list(a = a.merge1, b = b.merge1), method = "subtract", params="");
a.sub2 <- bedr.subtract.region(a.merge1, b.merge1);

### in.region
is.region <- in.region(a.merge1, b.merge1);
#is.region <- a.merge1 %in.region% b.merge1
### intersect 
# note for bedtools its recommended to bedr.sort.regions before intersect for faster processing
# also if regions are not merged this can cause unexpected behaviour
a.int1 <- bedr(input = list(a = a.sort1, b = b.sort1), method = "intersect", params = "-loj");
a.int1 <- bedr(input = list(a = a.sort1, b = b.sort1), method="intersect",params ="-loj -sorted");
a.int2 <- bedr(input = list(a = a.merge1, b = b.merge1), method="intersect",params="-loj -sorted");
a.int3 <- bedr.join.region(a.merge1, b.merge1);

### multiple join
d <- get.random.regions(100, chr="chr1", sort = TRUE);
a.mult <- bedr.join.multiple.region(x = list(a.merge1,b.merge1,bedr.sort.region(d)));

## Not run: 
  ### groupby 
  # note the "g" column number is based on bed format i.e. first three columns chr, start, stop
  # note the use of first, first, last on the region columns i.e. the union of the regions
  # note currently missing values are not dealt with in bedtools.  also the 5th column is 
  # assumed to be "score" and gets a default "-1" not a "."
  cnv.gene <- bedr(
    input = list(i=cnv.gene), method = "groupby", params = paste(
      "-g 16 -c ", 
      paste(1:15, collapse = ","), 
      " -o ", "first,first,last, ", 
      paste(rep("sum",12), collapse = ","), 
      sep = ""
      )
    );

  ### example 1
  ###  workflow adding gene names to exome sequencing target file
  # download refseq genes from ucsc or query biomart for ensemble gene names.  
  # format them in basic bed format.
  # sort, merge target
  # sort, merge -nms target.  Overlapping genes/features get merged.  
  # this may not be ideal if there are some really big features.
  # intersect -loj target, genes.
  # alternatively, do not merge the target and apply the merge after the intersect.  
  # this will provide precision at the level of the exon.
  
## End(Not run)
}

Example output

sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied
sh: 1: cannot create /dev/null: Permission denied


######################
#### bedr v1.0.3 ####
######################

checking binary availability...
  * Checking path for bedtools... FAIL
  * Checking path for bedops... FAIL
  * Checking path for tabix... FAIL
tests and examples will be skipped on R CMD check if binaries are missing

  * Checking path for bedtools... sh: 1: cannot create /dev/null: Permission denied
FAIL

bedr documentation built on May 2, 2019, 11:36 a.m.