R: Reads a clonotype_table and returns a data frame.

read_clonotypes {clonotypeR}

R Documentation

Reads a clonotype_table and returns a data frame.

Description

Reads a clonotype_table in a TAB-separated or OSCT format, and returns a data frame that has eight columns, for library name, V and J segments names, sequence read identifier, DNA, sequence quality, aminoacid sequence of the CDR3 region, mark for unproductive recombinations, and mark for ambiguous sequences.

Usage

read_clonotypes(filename, scores=TRUE, ...)

Arguments

`filename`	Path to the tabulation-delimited text file containing the extracted clonotypes.
`scores`	Set to false to load legacy data that did not contain “score” and “mapq” columns.
`...`	The rest of the arguments are passed to the `read.table()` function.

Value

`lib`	Library name (factor).
`V`	V segment name (factor).
`J`	J segment name (factor).
`score`	Alignment score (numeric).
`mapq`	Mapping quality (numeric). A sequence with a good alignment score will still have a low mapping quality if there are good alternative alignments to other V segments.
`read`	Sequence read identifier (character).
`dna`	DNA sequence of the CDR3 region (character).
`qual`	Quality values for the DNA sequence (character).
`pep`	Translation of the DNA sequence (character).
`unproductive`	Flag indicating stop codons or frame shifts (logical).
`ambiguous`	Flag indicating that the DNA sequences has ambiguous (“N”) nucleotides (logical).

Author(s)

Charles Plessy

Examples

clonotypes <- read_clonotypes(system.file('extdata', 'clonotypes.txt.gz', package = "clonotypeR"))

[Package clonotypeR version 1.1.3 Index]