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

In tcR: Advanced Data Analysis of Immune Receptor Repertoires

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")

## End(Not run)

tcR documentation built on July 2, 2020, 3:18 a.m.