Issues loading 10x data about immunarch

[vadimnazarov]

Hi @lothm2014

Thank you for using the package and helping the community!

You definitely use the correct file. However, you shouldn't pass the .format argument as immunarch automatically detects the file format. Can you please remove it and see if it works?

immdata <- repLoad("filtered_contig_annotations.csv")

[melanieloth]

Thanks for the quick response. That was successful. I did just want to pass along the following warnings when loading the data:

immdata<-repLoad(("filtered_contig_annotations.csv"))
== Step 1/3: loading repertoire files... ==
Processing "<initial>" ...
  -- Parsing "filtered_contig_annotations.csv" -- 10x (filt.contigs)
Warning: 151 parsing failures.
 row             col           expected               actual                              file
1041 NA              18 columns         27 columns           'filtered_contig_annotations.csv'
1042 is_cell         1/0/T/F/TRUE/FALSE TTRBV7-2             'filtered_contig_annotations.csv'
1042 high_confidence 1/0/T/F/TRUE/FALSE TRBJ1GACTrTCTGATTG-1 'filtered_contig_annotations.csv'
1042 length          a double           TrTCTGATTG-1         'filtered_contig_annotations.csv'
1042 full_length     1/0/T/F/TRUE/FALSE TRBV5-6              'filtered_contig_annotations.csv'
.... ............... .................. .................... .................................
See problems(...) for more details.

  [!] Removed 277 clonotypes with no nucleotide and amino acid CDR3 sequence.

== Step 2/3: checking metadata files and merging... ==
Processing "<initial>" ...
  -- Metadata file not found; creating a dummy metadata...

== Step 3/3: splitting data by barcodes and chain types... ==
Splitting repertoires by their chain type. Columns Chain and Source added to the metadata.
  -- Column Chain specifies chain types: TRA, TRB, etc.
  -- Column Source specifies the initial sample name for a repertoire after splitting by chain types
Done!
Warning message:
The following named parsers don't match the column names: barcode,is_cell,contig_id,high_confidence,length,chain,v_gene,d_gene,j_gene,c_gene,full_length,productive,cdr3,cdr3_nt,reads,umis,raw_clonotype_id,raw_consensus_id 

[vadimnazarov]

Thank you! Yes, we plan to fix the warnings, but not at the moment, I'm sorry. However, we would be glad to help anyone who seeks to fix them! Immunarch is finally on GitHub so we can work with the RepSeq / single-cell community even closer.