tcR (version 1.3)

parse.folder: Parse input table files with immune receptor repertoire data.

Description

Load the MITCR TCR data from the file with the given filename to a data frame. For general parser see parse.cloneset.

Usage

parse.file(.filename, .format = c('mitcr', 'mitcrbc', 'migec'), ...)
parse.file.list(.filenames, .format = c('mitcr', 'mitcrbc', 'migec'), .namelist = NA)
parse.folder(.folderpath, .format = c('mitcr', 'mitcrbc', 'migec'), ...)
parse.mitcr(.filename)
parse.mitcrbc(.filename)
parse.migec(.filename)

Arguments

.folderpath

Path to the folder with text cloneset files.

.format

String specifing input format of files. Parsers for MiTCR output and MiGEC output are available.

...

Parameters passed to parse.cloneset.

.filename

Path to the input file with cloneset data.

.filenames

Vector or list with paths to files with cloneset data.

.namelist

Either NA or character vector of length .filenames with names for output data frames.

Value

• Data frame with immune receptor repertoire data. Each row in this data frame corresponds to a clonotype. The data frame has following columns:

  - "Barcode.count" - number of barcodes (events, UMIs);

  - "Barcode.proportion" - proportion of barcodes (events, UMIs);

  - "Read.count" - number of reads;

  - "Read.proportion" - proportion of reads;

  - "CDR3.nucleotide.sequence" - CDR3 nucleotide sequence;

  - "CDR3.amino.acid.sequence" - CDR3 amino acid sequence;

  - "V.segments" - names of aligned Variable gene segments;

  - "J.segments" - names of aligned Joining gene segments;

  - "D.segments" - names of aligned Diversity gene segments;

  - "V.end" - last positions of aligned V gene segments (1-based);

  - "J.start" - first positions of aligned J gene segments (1-based);

  - "D5.end" - positions of D'5 end of aligned D gene segments (1-based);

  - "D3.end" - positions of D'3 end of aligned D gene segments (1-based);

  - "VD.insertions" - number of inserted nucleotides (N-nucleotides) at V-D junction (-1 for receptors with VJ recombination);

  - "DJ.insertions" - number of inserted nucleotides (N-nucleotides) at D-J junction (-1 for receptors with VJ recombination);

  - "Total.insertions" - total number of inserted nucleotides (number of N-nucleotides at V-J junction for receptors with VJ recombination).

See Also

parse.cloneset

Examples

# Parse file in "~/mitcr/immdata1.txt" as a MiTCR file.
immdata1 <- parse.file("~/mitcr/immdata1.txt", 'mitcr')
# Parse files "~/data/immdata1.txt" and "~/data/immdat2.txt" as MiGEC files.
immdata12 <- parse.file.list(c("~/data/immdata1.txt",
                             "~/data/immdata2.txt"), 'migec')
# Parse all files in "~/data/" as MiGEC files.
immdata <- parse.folder("~/data/", 'migec')