(hom_rate > 0.4) {: missing value where TRUE/FALSE needed

[stela2502]

Hi Numbat developers,

I am not used to run SNP analyses and am trying to apply your tool to our 10x data.
I have created the allele counts tar.gz file and am now trying to run the numbat_run step.
I have had other issues previousely and am therefore kind of sure that this error or something totally new:

Error in if (hom_rate > 0.4) {: missing value where TRUE/FALSE needed
Traceback:

1. runBatch(i)
2. numbat::run_numbat(subset, ref_hca, fread(df_allele_ATC2), genome = hg38,
   . t = 1e-05, ncores = 4, min_cells = 100, plot = TRUE, out_dir = paste(sep = ,
   . ./numbat_run_, sampleid, /, batch)) # at line 28-38 of file
3. bulk_subtrees %>% filter(sample == 0) %>% check_contam()
4. check_contam(.)

This error is thrown by this function and I fear that my data is simply lacking,

#' check inter-individual contamination
#' @param bulk dataframe Pseudobulk profile
#' @return NULL
#' @Keywords internal
check_contam = function(bulk) {

hom_rate = bulk %>% filter(DP >= 8) %>%
    {mean(na.omit(.$AR == 0 | .$AR == 1))}

if (hom_rate > 0.4) {
    msg = paste0(
        'High SNP contamination detected ',
        '(', round(hom_rate*100, 1), '%)',
        '. Please make sure that cells from only one individual are included in genotyping step.')
    message(msg)
    log_warn(msg)
}

}

Can you tell me how I can filter my data to get a working sample into your program?

Thank you very much!

/Stefan

[frstyang]

Hi, I'm facing the same issue. Were you able to resolve this problem, and if so, would you mind explaining a bit how?

Based on the location in the code where hom_rate is computed, the error seems to be because there aren't enough pseudobulks which pass the filtering in check_contam.

[teng-gao]

Seems like if the bulk df is empty after filtering by DP it will throw this error. Need to catch this case & throw a more informative error msg

Same as #210

In the mean time this probably means the dataset doesn't have enough SNP coverage..

[frstyang]

Thanks for the response! It turns out, I was running into this error because of a bug in my nextflow pipeline where the allelic data and expression data being fed into numbat were mismatched from different samples.