Parse input table files with the immune receptor repertoire data.

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Description

General parser for cloneset table files. Each column name has specific purpose (e.g., column for CDR3 nucleotide sequence or aligned gene segments), so you need to supply column names which has this purpose in your input data.

Usage

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parse.cloneset(.filename, .nuc.seq, .aa.seq, .reads, .barcodes, .vgenes,
  .jgenes, .dgenes, .vend, .jstart, .dalignments, .vd.insertions,
  .dj.insertions, .total.insertions, .skip = 0, .sep = "\t")

Arguments

.filename

Path to the input file with cloneset data.

.nuc.seq

Name of the column with CDR3 nucleotide sequences.

.aa.seq

Name of the column with CDR3 amino acid sequences.

.reads

Name of the column with counts of reads for each clonotype.

.barcodes

Name of the column with counts of barcodes (UMI, events) for each clonotype.

.vgenes

Name of the column with names of aligned Variable gene segments.

.jgenes

Name of the column with names of aligned Joining gene segments.

.dgenes

Name of the column with names of aligned Diversity gene segments.

.vend

Name of the column with last positions of aligned V gene segments.

.jstart

Name of the column with first positions of aligned J gene segments.

.dalignments

Character vector of length two that names columns with D5' and D3' end positions.

.vd.insertions

Name of the column with VD insertions for each clonotype.

.dj.insertions

Name of the column with DJ insertions for each clonotype.

.total.insertions

Name of the column with total number of insertions for each clonotype.

.skip

How many lines from beginning to skip.

.sep

Separator character.

Value

Data frame with immune receptor repertoire data. See parse.file for more details.

See Also

parse.file

Examples

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## Not run: 
# Parse file in "~/mitcr/immdata1.txt" as a MiTCR file.
immdata1 <- parse.file("~/mitcr/immdata1.txt", 'mitcr')

## End(Not run)

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