adapter_content {qckitfastq} | R Documentation

## Creates a sorted from most frequent to least frequent abundance table of adapters that are found to be present in the reads at greater than 0.1% of the reads. If output_file is selected then will save the entire set of adapters and counts. Only available for macOS/Linux due to dependency on C++14.

### Description

Creates a sorted from most frequent to least frequent abundance table of adapters that are found to be present in the reads at greater than 0.1% of the reads. If output_file is selected then will save the entire set of adapters and counts. Only available for macOS/Linux due to dependency on C++14.

### Usage

    adapter_content(infile, adapter_file = system.file("extdata",
      "adapters.txt", package = "qckitfastq"), output_file = NA)

### Arguments

`infile` | the path to a gzipped FASTQ file
`adapter_file` | Path to adapters.txt file. Default from package.
`output_file` | File to save data frame to. Default NA.

### Value

Sorted table of adapters and counts.

### Examples

    if(.Platform$OS.type != "windows") {
    infile <- system.file("extdata","test.fq.gz",
        package = "qckitfastq")
    adapter_content(infile)[1:5]
    }

[Package qckitfastq version 1.0.1 Index]