immunarch repLoad immdata<-repLoad(file_path) Error in `df[, vec_names]`:

[yueli8]

Hello,

Thank you for developing so nice software: immunarch.

Thank you in advance for great help!

Best,

Yue

Please see atached files. P61_Tumor.csv P61_Blood.csv P60_Tumor.csv P60_Blood.csv P58_Tumor.csv P58_Blood.csv P57_Tumor.csv P57_Blood.csv metadata.txt

setwd("~/gse162499")
file_path="~/gse162499/immunarch_data/immunarch"
immdata<-repLoad(file_path)

== Step 1/3: loading repertoire files... ==

Processing "~/gse162499/immunarch_data/immunarch" ...
  -- [1/9] Parsing "/home/yueli/gse162499/immunarch_data/immunarch/metadata.txt" -- metadata
  -- [2/9] Parsing "/home/yueli/gse162499/immunarch_data/immunarch/P57_Blood.csv" -- 10x (filt.contigs)                                                                                   
Error in `df[, vec_names]`:                                                                                                                                                               
! Can't subset columns that don't exist.
✖ Columns `cdr1_nt`, `cdr1`, `cdr2_nt`, `cdr2`, `fwr1_nt`, etc. don't exist.
Run `rlang::last_trace()` to see where the error occurred.

[yueli8]

It works.

t3_filtered_contig_annotations.csv t2_filtered_contig_annotations.csv t1_filtered_contig_annotations.csv p3_filtered_contig_annotations.csv p2_filtered_contig_annotations.csv p1_filtered_contig_annotations.csv metadata.txt

library(immunarch)
setwd("~/liuzhuqing/immunarch")
file_path="~/liuzhuqing/immunarch/data"
immdata<-repLoad(file_path)

[savitaj]

Hi @immunomind,

Thanks so much for developing this wonderful software. One of my favourite packages for BCR/TCR analysis.

I am getting the same error, has this been fixed? I wasn't facing this before.

Thanks in advance! Savita

[savitaj]

Hi @immunomind,

Thanks so much for developing this wonderful software. One of my favourite packages for BCR/TCR analysis.

I am getting the same error, has this been fixed? I wasn't facing this before.

Error in df[, vec_names]: ! Can't subset columns that don't exist. x Columns cdr1_nt, cdr1, cdr2_nt, cdr2, fwr1_nt, etc. don't exist. Backtrace:

1. immunarch::repLoad(BCR.path, .mode = "paired")
2. immunarch (local) .process_batch(batches[[batch_i]], .mode, .coding)
3. immunarch (local) .read_repertoire(.filepath, .mode, .coding, ...)
4. immunarch (local) parse_fun(.path, .mode, ...)
5. immunarch:::parse_repertoire(...)
6. tibble:::[.tbl_df(df, , vec_names) Execution halted

Thanks in advance! Savita

[vadimnazarov]

Hi Savita, what could you show what is inside the vec_names please?