tcR (version 2.2.4)

repLoad: Parse input files or folders with immune receptor repertoire data.

Description

Load the immune receptor repertoire data from the given input: either a file name, a list of file names, a name of the folder with repertoire files, or a list of folders with repertoire files. The folder / folders must contain only files with the specified format. Input files could be either text files or archived with gzip ("filename.txt.gz") or bzip2 ("filename.txt.bz2"). For a general parser of table files with cloneset data see parse.cloneset.

Parsers are available for: MiTCR ("mitcr"), MiTCR w/ UMIs ("mitcrbc"), MiGEC ("migec"), VDJtools ("vdjtools"), ImmunoSEQ ("immunoseq" or 'immunoseq2' for old and new formats respectively), MiXCR ("mixcr"), IMSEQ ("imseq") and tcR ("tcr", data frames saved with the `repSave()` function).

Output of MiXCR should contain either all hits or best hits for each gene segment.

Output of IMSEQ should be generated with parameter "-on". In this case there will be no positions of aligned gene segments in the output data frame due to restrictions of IMSEQ output.

tcR's data frames should be saved with the `repSave()` function.

For details on the tcR data frame format see parse.file.

Usage

repLoad(.path, .format = c("mitcr", "migec"))

Arguments

.path

Character vector with path to files and / or folders.

.format

String that specifies the input format.

See Also

parse.file

Examples

# NOT RUN {
datalist <- repLoad(c("file1.txt", "folder_with_files1", "another_folder"), "mixcr")
# }