topFreq: Top frequencies

In davidcoffey/LymphoSeq: Analyze high-throughput sequencing of T and B cell receptors

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)

davidcoffey/LymphoSeq documentation built on Dec. 31, 2019, 9:52 p.m.