Description Usage Arguments Details Value Author(s) References Examples
View source: R/adapterremoval.R
This function can be use to call wrapped AdapterRemoval
binary for adapters identifying.
1 | identify_adapters(file1, file2, ..., basename = NULL, overwrite = FALSE)
|
file1 |
|
file2 |
|
... |
Additional arguments to be passed on to the binaries. See below for details. |
basename |
|
overwrite |
|
All additional arguments in ... are interpreted as
additional parameters to be passed on to
identify_adapters. All of them should be Character
or
Numeric
scalar. You can put all aditional
arguments in one Character
(e.g. "–threads 8") with white
space splited just like command line,
or put them in different Character
(e.g. "–threads","8").
Note that some arguments("–identify-adapters",
"–file1","–file2","–basename") to the
identify_adapters are invalid if they are already handled as
explicit function arguments. See the output of
adapterremoval_usage()
for details about available parameters.
An invisible Character
vector of adapters for each mate.
Zheng Wei
Schubert, Lindgreen, and Orlando (2016). AdapterRemoval v2: rapid adapter trimming, identification, and read merging. BMC Research Notes, 12;9(1):88.
1 2 3 4 5 6 7 | td <- tempdir()
reads_1 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_1.fq")
reads_2 <- system.file(package="Rbowtie2", "extdata", "adrm", "reads_2.fq")
adapters <- identify_adapters(file1=reads_1,file2=reads_2,
basename = file.path(td,"reads")
,"--threads 2",overwrite=TRUE)
adapters
|
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