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Issue with Reconstructing Bcell clonal lineages
Hi,
I am working with mouse B cell repertoires processed with MIXCR (for consistency for this project I am still using MIXCR v3.0.13). The alignment was done on the VDJregion so I can export all the required fields for the downstream analysis. My file has the following fields present: cloneId, cloneCount, cloneFraction, nSeqCDR3, nSeqCDR1, nSeqCDR2, nSeqFR1, nSeqFR2, nSeqFR3, nSeqFR4, aaSeqCDR3, bestVHit, bestDHit, bestJHit, bestCHit. I am able to load the data in R with immunarch and look into it in terms of diversity etc... But now I would like to reconstruct Bcell clonal lineages. When I use the following command I am getting the error below. Any insight would be very helpful, Thanks !
best
Julien
command: Lineages_align <- immdata_mixcr$data %>% seqCluster(seqDist(immdata_mixcr$data, .col = 'CDR3.nt', .group_by_seqLength = TRUE), .perc_similarity = 0.8) %>% repGermline(.threads = 2, .species = "MusMusculus") %>% repAlignLineage(.min_lineage_sequences = 6, .align_threads = 2, .nofail = TRUE)
error:
Error in map2():
ℹ In index: 1.
ℹ With name: clones_100.
Caused by error in get():
! object 'generate_germline_sequence' not found
Run rlang::last_error() to see where the error occurred.
Warning messages:
1: There was 1 warning in mutate().
ℹ In argument: length_value = map_chr(.y, ~ifelse(all(.x == .x[1]), yes = .x[1], no = glue("range_{min(.x)}:{max(.x)}"))).
Caused by warning:
! Automatic coercion from integer to character was deprecated in purrr 1.0.0.
ℹ Please use an explicit call to as.character() within map_chr() instead.
ℹ The deprecated feature was likely used in the immunarch package.
Please report the issue at https://github.com/immunomind/immunarch/issues.
This warning is displayed once every 8 hours.
Call lifecycle::last_lifecycle_warnings() to see where this warning was generated.
2: In seqCluster(., seqDist(immdata_mixcr$data, .col = "CDR3.nt", .group_by_seqLength = TRUE), :
Number of sequence provided in .data and .dist are not matching!
System: Mac osx 12.3.1, R 4.2.0 Immunarch 0.9.0
