bowtie2-build {Rbowtie2} | R Documentation |
This function can be use to call wrapped bowtie2-build
binary
bowtie2_build(references, bt2Index, ..., overwrite = FALSE)
references |
|
bt2Index |
|
... |
Additional arguments to be passed on to the binaries. See below for details. |
overwrite |
|
All additional arguments in ... are interpreted as additional
parameters to be passed on to
bowtie2_build. All of them should be Character
or
Numeric
scalar. You can put all aditional
arguments in one Character
(e.g. "–threads 8 –quiet") with white
space splited just like command line,
or put them in different Character
(e.g. "–threads","8","–quiet").
See the output of
bowtie2_build_usage()
for details about available parameters.
An invisible Integer
of call status.
The value is 0 when there is not any mistakes
Otherwise the value is non-zero.
Zheng Wei
Langmead, B., & Salzberg, S. L. (2012). Fast gapped-read alignment with Bowtie 2. Nature methods, 9(4), 357-359.
td <- tempdir() ## Building a bowtie2 index refs <- dir(system.file(package="Rbowtie2", "extdata", "bt2","refs"), full=TRUE) cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), "--threads 4 --quiet",overwrite=TRUE);cmdout ## Use additional arguments in another way cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), "--threads",4,"--quiet",overwrite=TRUE);cmdout ## The function will print the output ## during the process without "--quiet" argument. cmdout<-bowtie2_build(references=refs, bt2Index=file.path(td, "lambda_virus"), overwrite=TRUE);cmdout