.callbinary {Rbowtie2} | R Documentation |
Make system call for binaries
Description
Function that makes a system call for the bowtie binaries.
Note it is not intended to be used outside of the package.
Usage
.callbinary(
bin1,
args1,
op = NULL,
bin2 = NULL,
args2 = NULL,
path = NULL,
lang = NULL
)
Arguments
bin1 |
Character . The binary used for the system call.
|
args1 |
Character . The arguments to pass to the binary.
|
op |
Character . Optional: Generally used if needed to pipe to another binary.
|
bin2 |
Character . Optional: Another binary that can be used in the system call.
Generally the output of the first binary is piped to the this binary.
|
args2 |
Character Optional: The arguments to pass to the second binary.
|
path |
Character Optional: If passed to function, returns the path.
Needed for Rsamtools to convert from sam to bam.
|
lang |
Character . The interpreter used to execute the binary
|
Value
The output of the system call or the path provided.
Author(s)
Zheng Wei
[Package
Rbowtie2 version 2.0.0
Index]