read_clonotypes: Reads a clonotype_table and returns a data frame.

In charles-plessy/clonotypeR.old: High throughput analysis of T cell antigen receptor sequences

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

See Also

clonotype_table, is_unproductive, read.table, Order Switchable Column Table (OSCT, http://sourceforge.net/projects/osctf/)

Examples

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

charles-plessy/clonotypeR.old documentation built on May 13, 2019, 3:31 p.m.