% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/productive.R
\title{Productive sequences}
productive(sample, aggregate = "aminoAcid")
\item{sample}{A data frame consisting of antigen receptor sequencing data.
"aminoAcid", "count", and "frequencyCount" are required columns.}

\item{aggregate}{Indicates whether the values of "count", "frequencyCount", 
and "esimatedNumberGenomes" should be aggregated by amino acid or nucleotide 
sequence.  Acceptable values are "aminoAcid" or "nucleotide".  If "aminoAcid" 
is selected, then the resulting data frame will have columns corresponding to 
"aminoAcid", "count", "frequnecyCount", and "estimatedNumberGenomes" (if this 
column is available).  If "nucleotide" is selected then all columns in the 
original data frame will be present in the outputted data frame.  The difference in 
output is due to the fact that the same amino acid CDR3 sequence may be 
encoded by multiple unique nucleotide sequences with differing V, D, and J 
Returns a data frame of productive amino acid sequences with recomputed 
values for "count", "frequencyCount", and "esimatedNumberGenomes".  A 
productive sequences is defined as a sequence that is in frame and does not 
have an early stop codon.
Remove unproductive CDR3 sequences from a single data frame.
file.path <- system.file("extdata", "TCRB_sequencing", package = "LymphoSeq")

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

productive <- productive(sample = file.list[["TCRB_Day32_Unsorted"]], aggregate = "aminoAcid")