Description Usage Arguments Details Value Author(s) References Examples
View source: R/adapterremoval.R
This function can be use to call wrapped AdapterRemoval
binary.
1 2 3 |
file1 |
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... |
Additional arguments to be passed on to the binaries. See below for details. |
adapter1 |
|
output1 |
|
file2 |
|
adapter2 |
|
output2 |
|
basename |
|
interleaved |
|
overwrite |
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All additional arguments in ... are interpreted as additional
parameters to be passed on to
remove_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(
"–file1","–file2","–adapter1","–adapter2","–output1","–output2",
"–basename","–interleaved") 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 Integer
of call status.
The value is 0 when there is not any mistake.
Otherwise the value is non-zero.
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 8 9 10 11 12 13 14 | td <- tempdir()
# Identify adapters
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 3",overwrite=TRUE)
# Remove adapters
cmdout<-remove_adapters(file1=reads_1,file2=reads_2,adapter1 = adapters[1],
adapter2 = adapters[2],
output1=file.path(td,"reads_1.trimmed.fq"),
output2=file.path(td,"reads_2.trimmed.fq"),
basename=file.path(td,"reads.base"),overwrite=TRUE,"--threads 3");cmdout
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