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.
coding(.data)
noncoding(.data)
inframes(.data)
outofframes(.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.
Filtered data frame.
data(immdata)
immdata_cod <- coding(immdata$data)
immdata_cod1 <- coding(immdata$data[[1]])