R: Filter out coding and non-coding clonotype sequences

coding {immunarch} | R Documentation

## Filter out coding and non-coding clonotype sequences

### Description

Filter out clonotypes with non-coding, coding, in-frame or out-of-frame CDR3 sequences:

'coding()' - remove all non-coding sequences (i.e., remove all sequences with stop codons and frame shifts);

'noncoding()' - remove all coding sequences (i.e., leave sequences with stop codons and frame shifts only);

'inframes()' - remove all out-of-frame sequences (i.e., remove all sequences with frame shifts);

'outofframes()' - remove all in-frame sequences (i.e., leave sequences with frame shifts only).

Note: the function will remove all clonotypes sequences with NAs in the CDR3 amino acid column.

### Usage

    coding(.data)

    noncoding(.data)

    inframes(.data)

    outofframes(.data)

### Arguments

`.data` | The data to be processed. Can be data.frame, data.table, or a list of these objects. Every object must have columns in the immunarch compatible format. immunarch_data_format Competent users may provide advanced data representations: DBI database connections, Apache Spark DataFrame from copy_to or a list of these objects. They are supported with the same limitations as basic objects. Note: each connection must represent a separate repertoire.

### Value

Filtered data frame.

### Examples

    data(immdata)
    immdata_cod <- coding(immdata$data)
    immdata_cod1 <- coding(immdata$data[[1]])

[Package immunarch version 0.6.5 Index]