Error running estimateAbundance
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)
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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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- changed status to resolved
No worries. Who has not had issues with NAs? :) Glad that this worked.
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Hi Miriam. Does the column
c_call
exist? Does it contain any rows withc_call=NA`
? Maybe NAs are the issue. If NAs are not the issue, please send me to immcantation@googlegroups.com example data to reproduce the error and I will debug this.