readImmunoSeq: Read ImmunoSeq files

In elulu3/LymphoSeqTest: Analyze high-throughput sequencing of T and B cell receptors

Read ImmunoSeq files

Description

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)

getStandard(clone_file, airr_fields, matching_fields)

readFiles(clone_file, empty_airr_frame, matching_fields, progress)

iReceptorFormat(clone_frame)

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.
clone_file	.tsv file containing results from AIRRSeq pipeline
airr_fields	A character vector of MiAIRR headers
clone_frame	An AIRR compliant tibble

Value

Returns a tibble with MiAIRR headers and repertoire_id

Tibble of given data with MiAIRR fields

Tibble in MiAIRR format

Tibble in iReceptor format

Get standard headers

Retrives MiAIRR standard compliant fields from the clone files

Read clone file from path

Given the path to a single AIRRSeq clone file, generate MiAIRR compliant tibble.

Get iReceptor standard format

Returns a tibble that is compliant with the iReceptor repertoire format.

elulu3/LymphoSeqTest documentation built on Aug. 27, 2022, 5:47 a.m.