topFreq {LymphoSeq} | R Documentation

## Top frequencies

### Description

Creates a data frame of the top productive amino acid sequences that have a specified minimum frequency threshold and reports the number of samples that the sequence appears in along with the minimum, maximum, and mean frequency across all samples. For T cell receptor beta sequences, the % prevalence and antigen specificity of that sequence is also provided.

### Usage

    topFreq(productive.aa, percent = 0.1)

### Arguments

`productive.aa` | A list data frames of of productive amino acid sequences imported using the function LymphoSeq function productiveSeq where the aggregate parameter was set to "aminoAcid".
`percent` | The minimum % frequency that the sequence appears in any of the listed samples.

### Value

A data frame of amino acid sequences and the number of samples that the sequence appears in along with the minimum, maximum, and mean frequency across all samples. For T cell receptor beta sequences, additionally reported is the % prevalence that the sequence appears in 55 healthy donor blood samples. Also provided is the antigen specificity of that sequence if known by comparing it to a database of previously reported sequences in the literature. The prevalenceTRB and publishedTRB databases are located in a separate package called LymphoSeqDB that should be loaded automatically.

### See Also

Refer to the LymphoSeqDB package for details regarding the prevalenceTRB and publishedTRB database.

### Examples

    file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

    file.list <- readImmunoSeq(path = file.path)

    productive.aa <- productiveSeq(file.list = file.list, aggregate = "aminoAcid")

    top.freq <- topFreq(productive.aa = productive.aa, percent = 0.1)

[Package LymphoSeq version 1.20.0 Index]