topFreq: Top frequencies

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

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 \ and antigen specificity of that sequence is also provided.

Usage

topFreq(productive_table, frequency = 0.1)

Arguments

productive_table	A tibble of productive amino acid sequences imported using the function LymphoSeq function productiveSeq where the aggregate parameter was set to "junction_aa".
frequency	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 \ Also provided is the antigen specificity of that sequence if known by comparing it to a database of previously reported sequences in the literature.

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.