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Read ImmunoSeq files

Source: R/readImmunoSeq.R
readImmunoSeq.Rd

readImmunoSeq() Imports tab-separated value (.tsv) files exported by the Adaptive Biotechnologies ImmunoSEQ analyzer, BGI IR-SEQ, MiXCR and stores them as MiAIRR compliant tibble.

Usage

readImmunoSeq(path, recursive = FALSE, threads = parallel::detectCores()/2)

Arguments

path

Path to the directory containing tab-delimited files. Only files with the extension .tsv are imported. The names of the data frames are the same as names of the files.

recursive

A Boolean value

  • TRUE : the function will recursively search directory for all .tsv files

  • FALSE (the default): Open file using path

threads

Number of threads.

Value

Returns a tibble with MiAIRR headers and repertoire_id

Examples

file_path <- system.file("extdata", "TCRB_sequencing",
 package = "LymphoSeq2")
study_table <- LymphoSeq2::readImmunoSeq(
  path = file_path, recursive = FALSE,
  threads = 1
)
study_table <- LymphoSeq2::topSeqs(study_table, top = 100)