mixcr_TRB is a simple R wrapper function for MIXCR (Milaboratory) for standard processing of multiple TRB repseq files (5'RACE derived) usage:
mixcr_TRB(samples, outputFolder, new_meta_features, return_cloneset_list=T )
Arguments:
samples - character string, path to a tab-delimited metafile. Headers are required, columns id, R1, R2 are mandatory. Can also take a data.frame as input.
| id | R1 | R2 | Any_optional_features |
|---|---|---|---|
| Sample_X | /data/SX_R1.fastq.gz | /data/SX_R2.fastq.gz | Healthy |
| Sample_Y | /data/SX_R1.fastq.gz | /data/SX_R2.fastq.gz | AS |
| Sample_5 | ... | ... | ... |
outputFolder - path to outputFolder
new_meta_features - character vector, containing colnames for features to be saved in new meta file. By default - id, paths to cloneset files and other optional features are used, while R1 and R2 are dropped.
return_cloneset_list - boolean, if T all clonesets are returned as a list of data.tables. Else empty vector is returned
Output:
In outputFolder following subdirectories are created: alignments/, clonesets/, export/, corresponding to mixcr conventional steps Additionally, new metafile with ids and paths to clonesets is created.