coding: Filter out coding and non-coding clonotype sequences

Description Usage Arguments Value Examples

View source: R/preprocessing.R

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

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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

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

immunarch documentation built on July 2, 2020, 1:57 a.m.