Error running estimateAbundance

Issue #101 resolved
Miriam Llorian created an issue

Hi, thank you very much for such a great tool. I’m having issues running estimateAbundance, if I select group="c_call" I get the error below, however if I leave group=NULL there's no error. I've tried to find out where it breaks and it seems that it does in boot_mat <- bootstrapAbundance(abund_obs, n, nboot = nboot, method = "before") however I don’t know how to address the error. I’d appreciate any suggestion you may have. Thank you!

estimateAbundance( data , group="c_call", ci=0.95, nboot=100)
Error in if (f2 > 0)  { : missing value where TRUE/FALSE needed
In addition: Warning message:
In estimateAbundance(data_h[[11]], group = "c_call", ci = 0.95,  :
Not all groups passed threshold min_n=30. Excluded: IGHE

where data looks like:

 head(data_h[[11]])
# A tibble: 6 × 62
  sequence_id sequence rev_comp productive v_call d_call j_call sequence_alignm…
  <chr>       <chr>    <lgl>    <lgl>      <chr>  <chr>  <chr>  <chr>           
1 CTTAACTCAA… GACAACA… FALSE    TRUE       IGHV1… IGHD2… IGHJ4… CAGATTCAGCTGCAG…
2 CCTTCGACAC… AACATAA… FALSE    TRUE       IGHV1… IGHD3… IGHJ4… CAGGTCCAACTGCAG…
3 GATCGCGGTT… TGGGGAG… FALSE    TRUE       IGHV1… IGHD2… IGHJ1… GAGGTCCAGCTGCAA…
4 TGTGGTACAG… GAACCTA… FALSE    TRUE       IGHV1… IGHD1… IGHJ2… CAGGTTCAGCTGCAG…
5 CGATTGACAG… GGAACCT… FALSE    TRUE       IGHV1… IGHD2… IGHJ2… CAGGTTCAGCTGCAG…
6 AGCAGCCGTA… GGGGAAC… FALSE    TRUE       IGHV1… IGHD1… IGHJ2… CAGGTTCAGCTGCAG…
# … with 54 more variables: germline_alignment <chr>, junction <chr>,
#   junction_aa <chr>, v_cigar <chr>, d_cigar <chr>, j_cigar <chr>,
#   stop_codon <lgl>, vj_in_frame <lgl>, locus <chr>, junction_length <dbl>,
#   np1_length <dbl>, np2_length <dbl>, v_sequence_start <dbl>,
#   v_sequence_end <dbl>, v_germline_start <dbl>, v_germline_end <dbl>,
#   d_sequence_start <dbl>, d_sequence_end <dbl>, d_germline_start <dbl>,
#   d_germline_end <dbl>, j_sequence_start <dbl>, j_sequence_end <dbl>, …

Comments (3)

  1. Miriam Llorian reporter

    Hi, thank you for your fast reply. You are right, there're NAs on my col "c_call", I can confirm that after removing those rows, estimateAbundance runs properly. Thank you for your help and apologies for not noticing the "NAs", my bad.

    Thank you again

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