returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType #306

Guan06 · 2024-09-28T20:31:27Z

Describe the bug
I am tring to get the count table of relative abundance of some disease related samples, all good when loading with counts = FALSE but errors occur when setting counts to TRUE.

To Reproduce
I have version curatedMetagenomicData_3.8.0

Blow is the scripts that got errors:

study <- "IaniroG_2022"

  samples <- filter(sampleMetadata, 
                 study_name == study) |>
    filter(body_site=="stool") |>
    select(where(~ !all(is.na(.x))))
  
  print(study)
  filter_lst <- c("acute_diarrhoea", "CDI", "FMT", "IBD", "control")
  samples <- samples[(samples$study_condition %in% filter_lst) &
                       (samples$country != "CHN"), ]
  ra_2022 <- returnSamples(samples, counts = TRUE,
                      dataType = "relative_abundance", rownames = "long")

Expected behavior
Return of a count table.

Additional context
Error message:
Error in validObject(.Object) :
invalid class “SummarizedExperiment” object:
nb of cols in 'assay' (0) must equal nb of rows in 'colData' (165)

The text was updated successfully, but these errors were encountered:

lwaldron · 2025-01-27T13:58:54Z

Thank you for the report, and I'm terribly sorry for the delay. @schifferl I can reproduce this bug, it seems to be an invalid replacement of the assay in a SummarizedExperiment. I added to the example that it doesn't happen with the ?returnSamples example, maybe because it merges multiples datasets instead of using just one.

library(curatedMetagenomicData)
library(dplyr)

study <- "IaniroG_2022"

samples <- dplyr::filter(sampleMetadata, 
                  study_name == study) |>
  filter(body_site=="stool") |>
  select(where(~ !all(is.na(.x))))

filter_lst <- c("acute_diarrhoea", "CDI", "FMT", "IBD", "control")

samples <- samples[(samples$study_condition %in% filter_lst) &
                     (samples$country != "CHN"), ]

returnSamples(samples, counts = TRUE, dataType = "relative_abundance")
#> 
#> $`2022-10-19.IaniroG_2022.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#>   k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> Error in validObject(.Object): invalid class "SummarizedExperiment" object: 
#>     nb of cols in 'assay' (0) must equal nb of rows in 'colData' (165)
returnSamples(samples, counts = FALSE, dataType = "relative_abundance")
#> 
#> $`2022-10-19.IaniroG_2022.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#>   k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> class: TreeSummarizedExperiment 
#> dim: 637 135 
#> metadata(0):
#> assays(1): relative_abundance
#> rownames(637):
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Clostridiaceae|g__Clostridium|s__Clostridium_sp_CAG_413
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_bromii
#>   ...
#>   k__Bacteria|p__Firmicutes|c__Negativicutes|o__Selenomonadales|f__Selenomonadaceae|g__Centipeda|s__Centipeda_periodontii
#>   k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_buccalis
#> rowData names(7): superkingdom phylum ... genus species
#> colnames(135): Sample_S25223_FMT_01_t7 Sample_S25235_FMT_09_t7 ...
#>   R5_290108_t7 R6_271006_t30
#> colData names(17): study_name subject_id ... subcohort fmt_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (637 rows)
#> rowTree: 1 phylo tree(s) (10430 leaves)
#> colLinks: NULL
#> colTree: NULL

# However the dataset from examples in ?returnSamples doesn't have the same problem:

sampleMetadata |>
  dplyr::filter(age >= 18) |>
  dplyr::filter(!base::is.na(alcohol)) |>
  dplyr::filter(body_site == "stool") |>
  dplyr::select(where(~ !base::all(base::is.na(.x)))) |>
  returnSamples(dataType="relative_abundance", counts = TRUE)
#> 
#> $`2021-10-14.KaurK_2020.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#> $`2021-03-31.KeohaneDM_2020.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#> $`2021-03-31.QinN_2014.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#>   k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> $`2021-03-31.ThomasAM_2018a.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Bacillales|f__Bacillales_unclassified|g__Gemella|s__Gemella_bergeri
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#>   k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> $`2021-03-31.XieH_2016.relative_abundance`
#> dropping rows without rowTree matches:
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Atopobiaceae|g__Olsenella|s__Olsenella_profusa
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Collinsella|s__Collinsella_stercoris
#>   k__Bacteria|p__Actinobacteria|c__Coriobacteriia|o__Coriobacteriales|f__Coriobacteriaceae|g__Enorma|s__[Collinsella]_massiliensis
#>   k__Bacteria|p__Firmicutes|c__Bacilli|o__Lactobacillales|f__Carnobacteriaceae|g__Granulicatella|s__Granulicatella_elegans
#>   k__Bacteria|p__Firmicutes|c__Clostridia|o__Clostridiales|f__Ruminococcaceae|g__Ruminococcus|s__Ruminococcus_champanellensis
#>   k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae|g__Bulleidia|s__Bulleidia_extructa
#>   k__Bacteria|p__Proteobacteria|c__Betaproteobacteria|o__Burkholderiales|f__Sutterellaceae|g__Sutterella|s__Sutterella_parvirubra
#>   k__Bacteria|p__Synergistetes|c__Synergistia|o__Synergistales|f__Synergistaceae|g__Cloacibacillus|s__Cloacibacillus_evryensis
#> Warning: There was 1 warning in `mutate()`.
#> ℹ In argument: `across(.fns = ~replace_na(.x, 0))`.
#> Caused by warning:
#> ! Using `across()` without supplying `.cols` was deprecated in dplyr 1.1.0.
#> ℹ Please supply `.cols` instead.
#> class: TreeSummarizedExperiment 
#> dim: 833 702 
#> metadata(0):
#> assays(1): relative_abundance
#> rownames(833):
#>   k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_copri
#>   k__Bacteria|p__Bacteroidetes|c__Bacteroidia|o__Bacteroidales|f__Prevotellaceae|g__Prevotella|s__Prevotella_sp_CAG_520
#>   ...
#>   k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_aurimucosum
#>   k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_coyleae
#> rowData names(7): superkingdom phylum ... genus species
#> colnames(702): JAS_1 JAS_10 ... YSZC12003_37879 YSZC12003_37880
#> colData names(45): study_name subject_id ... inr zigosity
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> rowLinks: a LinkDataFrame (833 rows)
#> rowTree: 1 phylo tree(s) (10430 leaves)
#> colLinks: NULL
#> colTree: NULL

devtools::session_info()
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#>  date     2025-01-27
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^{Created on 2025-01-27 with reprex v2.1.1}

schifferl · 2025-02-08T21:21:56Z

This is a curation issue that is transmitted to cMD from cMDC whereby sampleMetadata[["number_reads"]] is missing for some studies due to trailing zeros in the curated TSV files. That issue is resolved by waldronlab/curatedMetagenomicDataCuration#82 and then the sampleMetadata object is updated in #311. When those PRs are merged, this issue can be closed.

Guan06 added the Bug Report label Sep 28, 2024

Guan06 assigned schifferl Sep 28, 2024

Guan06 changed the title ~~returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' aataType~~ returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType Sep 28, 2024

schifferl mentioned this issue Feb 8, 2025

update sampleMetadata object #311

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returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType #306

returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType #306

Guan06 commented Sep 28, 2024

lwaldron commented Jan 27, 2025

schifferl commented Feb 8, 2025

returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType #306

returnSamples() error when setting 'counts = TRUE' for 'relative_abundance' dataType #306

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Guan06 commented Sep 28, 2024

lwaldron commented Jan 27, 2025

schifferl commented Feb 8, 2025