parseFile {powerTCR}R Documentation

Load in and parse TCR data files for use by powerTCR

Description

These functions leverage the parse.file and parse.folder functions from the tcR package. They are wrappers that output data in the format taken by powerTCR.

Usage

parseFile(file, format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools',
                           'immunoseq', 'mixcr', 'imseq'),
                            inframe = TRUE)
parseFolder(folder, format = c('mitcr', 'mitcrbc', 'migec', 'vdjtools',
                               'immunoseq', 'mixcr','imseq'),
                                inframe = TRUE)

Arguments

file

Path to input file with TCR repertoire sample data.

folder

Path to input folder with one or more input files of TCR repertoire sample data.

format

String specifying the input format. The formats MiTCR ("mitcr"), MiTCR with UMIs ("mitcrbc"), MiGEC ("migec"), VDJtools ("vdjtools"), ImmunoSEQ (formats 1, 2, and 3), MiXCR ("mixcr"), and IMSEQ ("imseq") are currently supported. For more information on formatting, see parse.folder.

inframe

Logical. Should counts only from in-frame sequences be returned? Defaults to TRUE.

Value

parseFolder returns a list. Every element of the list is a vector of counts corresponding to a sample repertoire.

parseFile returns a vector of counts corresponding to the sample repertoire.

References

Nazarov, Vadim I., et al. "tcR: an R package for T cell receptor repertoire advanced data analysis." BMC bioinformatics 16.1 (2015): 175.


[Package powerTCR version 1.6.0 Index]