parse: Load in and parse TCR data files for use by powerTCR

In hillarykoch/powerTCR: Model-Based Comparative Analysis of the TCR Repertoire

Description

This function leverages repLoad functions from the immunarch package. They are wrappers that output data in the format taken by powerTCR.

Usage

parseFile(path, inframe = TRUE)

Arguments

path	Path to input file with TCR repertoire sample data.
inframe	Logical. Should counts only from in-frame sequences be returned? Defaults to TRUE.

Details

See the immunarch package on GitHub: https://github.com/immunomind/immunarch

Value

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.

hillarykoch/powerTCR documentation built on March 17, 2021, 8:05 p.m.