split_immunoseq_files: Split all-samples-in-one ImmunoSEQ files by sample

In charlotterich/immunarch_code: Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires in R

Description

Adaptive Biotechnologies ImmunoSEQ platform files are often downloaded as a big text file with receptor data for all samples from the experiment. Information about the source of each receptor is located in the "sample_name" column of the file. Such format is impractical for using in R analysis pipelines and require preprocessing to split the file into smaller files each corresponding to a specific sample. The split_immunoseq_files function splits the file into smaller files and writes them in the same ImmunoSEQ format to the output folder provided by the user.

If you want to just load the big file as separated data frames into R to use with immunarch, just use the repLoad function that automatically detectes the ImmunoSEQ format and splits the big file.

Usage

split_immunoseq_files(.big.file, .output.folder)

Arguments

.big.file	Path to the input ImmunoSEQ file with the "sample_name" column with information about receptors' source sample.
.output.folder	Path to the folder to write sample repertoires to.

See Also

repLoad

Examples

## Not run: 
# Split the file into smaller files
split_immunoseq_files("~/file/path/immunoseq_big.tsv", "~/file/path/experiment1")

# If you just want to load all files as separate data frames to use with immunarch,
# just use the repLoad function
immdata = repLoad("~/file/path/immunoseq_big.tsv")

## End(Not run)

charlotterich/immunarch_code documentation built on Jan. 24, 2020, 12:08 a.m.