productiveSeq: Productive sequences

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

Productive sequences

Usage

productiveSeq(study_table, aggregate = "junction_aa", prevalence = FALSE)

Arguments

study_table	A tibble consisting antigen receptor sequencing data imported by the LymphoSeq function readImmunoSeq. "junction_aa", "duplicate_count", and "duplicate_frequency" are required columns.
aggregate	Indicates whether the values of "duplicate_count", "duplicate_frequency", and "esimatedNumberGenomes" should be aggregated by amino acid or junction sequence. Acceptable values are "junction_aa" or "junction". If "junction_aa" is selected, then resulting data frame will have columns corresponding to junction_aa, duplicate_count, and duplicate_frequency. If "junction" is selected then all columns in the original list will be present in the outputted list. The difference in output is due to the fact that the same amino acid CDR3 sequence may be encoded by multiple unique junction sequences with differing V, D, and J genes.
prevalence	A Boolean value indicating if a new column should be added to each of the data frames giving the prevalence of each CDR3 amino acid sequence in 55 healthy donor peripheral blood samples. TRUE means the column is added and FALSE means it is not. Values range from 0 to 100\ 100\

Returns a list of data frames of productive amino acid sequences with recomputed values for "duplicate_count", "duplicate_frequency". A productive sequences is defined as a sequences that is in frame and does not have an early stop codon. productiveSeq Remove unproductive CDR3 sequences from a list of data frames. file_path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq2") stable <- readImmunoSeq(path = file_path) atable <- productiveSeq(study_table = stable, aggregate = "junction_aa", prevalence = TRUE)

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