read_clonotypes

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Description

Reads a clonotype_table and returns a data frame.

Usage

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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.

Details

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.

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).

See Also

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

Examples

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