ReadTrust | R Documentation |
ReadTrust
reads AIRR file and/or barcode_report/report file generated by TRUST4.
Generally
AIRR file: airr.tsv, barcode_airr.tsv (from TRUST4);
barcode_report file: barcode_report.tsv;
report file: report.tsv.
(.gz supported)
AIRR + barcode_report:
ReadTrust
will read AIRR and add it a 'cdr3_germline_similarity' column based on barcode_report.
only one file:
ReadTrust
will return a data.frame for this file.
AIRR/barcode_report + report:
ReadTrust
will ignore report file when either AIRR or barcode_report file is given.
ReadTrust( airr_file = NULL, barcode_report_file = NULL, report_file = NULL, verbose = TRUE )
airr_file |
character. Path to AIRR file. |
barcode_report_file |
character. Path to barcode_report file generated by TRUST4. |
report_file |
character. Path to report file generated by TRUST4. |
verbose |
logical. Print progress. Default is TRUE. |
A VDJ information data.frame
# file paths airr_file = system.file('extdata', 'TRUST4_airr.tsv.gz', package = 'TrustVDJ') barcode_report_file = system.file('extdata', 'TRUST4_barcode_report.tsv.gz', package = 'TrustVDJ') report_file = system.file('extdata', 'TRUST4_report.tsv.gz', package = 'TrustVDJ') # both AIRR and barcode_report data = ReadTrust(airr_file = airr_file, barcode_report_file = barcode_report_file) head(data) # only AIRR data = ReadTrust(airr_file = airr_file) head(data) # only barcode_report data = ReadTrust(barcode_report_file = barcode_report_file) head(data) # only report data = ReadTrust(report_file = report_file) head(data)
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