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Error using use_total in zero_low_counts command #227

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jarrodscott opened this issue Mar 23, 2018 · 4 comments

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@jarrodscott
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commented Mar 23, 2018

Hi @zachary-foster !

I am encountering an error when using use_total in zero_low_counts. I get this error using my data as well the hmp data

here is the code (from your tutorial)

print(hmp_otus)
print(hmp_samples)
obj2 <- parse_tax_data(hmp_otus, class_cols = "lineage", class_sep = ";", class_key = c(tax_rank = "info", tax_name = "taxon_name"), class_regex = "^(.+)__(.+)$")
print(obj2)
obj2$data$tax_data <- zero_low_counts(obj2, "tax_data", use_total = TRUE, min_count = 5)

and I get the following error:

Error in if (all(!is_greater_than_max)) { : missing value where TRUE/FALSE needed

The error persist no matter what value I use for min_counts when use_total = TRUE. If I use the default setting use_total = FALSE I can process the dataset completely following the tutorial.

Using:
R version 3.3.3 (2017-03-06) -- "Another Canoe"
metacoder verison 0.2.0.9011
OSX 10.10.5

@zachary-foster

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commented Mar 23, 2018

Thanks for the report!

I think I have it fixed. Try to install the dev version and see if it goes away:

devtools::install_github("ropensci/taxa")
devtools::install_github("grunwaldlab/metacoder")
@jarrodscott

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commented Mar 23, 2018

@jarrodscott

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commented Mar 24, 2018

that works! Thanks @zachary-foster

@zachary-foster

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commented Mar 26, 2018

Cool thanks!

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