Error in -create.label [...] invalid argument to unary operator

[borexino]

My code is here:

library(SIAMCAT)
library(phyloseq)
library(microbiome)

# Load my data
load("~/Data/PSM.RData")

# Same taxaonomic rank
pseq_genus <- phyloseq::tax_glom(psm, taxrank = "Genus")

# Log10 normalization
feat <- abundances(pseq_genus)
feat <- log10(feat + 1)

# My MetaData
meta <- pseq_genus@sam_data
meta <- data.frame(meta[,c("Sex", "AgeYrs", "Site", "Smoking", "BioProject", "size_MB")])
meta$Sex <- factor(meta$Sex)
label.meta <- - create.label(meta=meta,
                             label="Sex", case="female") 

Error got:

Label used as case:
   female
Label used as control:
   male
+ finished create.label.from.metadata in 0.001 s
Error in -create.label(meta = meta, label = "Sex", case = "female") : 
  invalid argument to unary operator

Dataframes structure/summary:

str(feat)

num [1:134, 1:148] 3.37 0 0 2.22 0 ...
- attr(*, "dimnames")=List of 2
..$ : chr [1:134] "OTU_001_Genus_Streptococcus" "OTU_002_Genus_Porphyromonas" "OTU_003_Genus_Prevotella_7" "OTU_004_Genus_Fusobacterium" ...
..$ : chr [1:148] "ERR494388" "ERR494389" "ERR494391" "ERR494392" ...

str(meta)

'data.frame':   148 obs. of  6 variables:
$ Sex       : Factor w/ 2 levels "female","male": 1 1 1 1 1 1 1 1 1 1 ...
$ AgeYrs    : int  41 41 56 56 19 19 44 44 46 46 ...
$ Site      : chr  "Subgingival" "Plaque" "Subgingival" "Plaque" ...
$ Smoking   : chr  NA NA NA NA ...
$ BioProject: chr  "PRJEB6047" "PRJEB6047" "PRJEB6047" "PRJEB6047" ...
$ size_MB   : chr  "7" "19" "18" "9" ...

sessionInfo()

R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

locale: [1] it_IT.UTF-8/it_IT.UTF-8/it_IT.UTF-8/C/it_IT.UTF-8/C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] microbiome_1.14.0 ggplot2_3.3.5 SIAMCAT_1.99.3 mlr3_0.13.3 phyloseq_1.36.0

loaded via a namespace (and not attached): [1] nlme_3.1-157 matrixStats_0.61.0 bitops_1.0-7 progress_1.2.2 RColorBrewer_1.1-2
[6] bbotk_0.5.2 PRROC_1.3.1 GenomeInfoDb_1.28.4 numDeriv_2016.8-1.1 mlr3learners_0.5.2
[11] tools_4.1.0 backports_1.4.1 utf8_1.2.2 R6_2.5.1 vegan_2.5-7
[16] DBI_1.1.2 BiocGenerics_0.38.0 mgcv_1.8-39 colorspace_2.0-3 permute_0.9-7
[21] rhdf5filters_1.4.0 ade4_1.7-18 withr_2.5.0 mlr3misc_0.10.0 prettyunits_1.1.1
[26] tidyselect_1.1.2 gridExtra_2.3 compiler_4.1.0 glmnet_4.1-3 cli_3.2.0
[31] Biobase_2.52.0 lgr_0.4.3 scales_1.1.1 checkmate_2.0.0 palmerpenguins_0.1.0
[36] mlr3tuning_0.12.1 stringr_1.4.0 digest_0.6.29 minqa_1.2.4 paradox_0.8.0
[41] XVector_0.32.0 pkgconfig_2.0.3 parallelly_1.30.0 lme4_1.1-28 rlang_1.0.2
[46] rstudioapi_0.13 shape_1.4.6 generics_0.1.2 jsonlite_1.8.0 dplyr_1.0.8
[51] RCurl_1.98-1.6 magrittr_2.0.2 GenomeInfoDbData_1.2.6 biomformat_1.20.0 Matrix_1.4-1
[56] Rcpp_1.0.8.3 munsell_0.5.0 S4Vectors_0.30.2 Rhdf5lib_1.14.2 fansi_1.0.3
[61] ape_5.6-2 lifecycle_1.0.1 infotheo_1.2.0 pROC_1.18.0 stringi_1.7.6
[66] MASS_7.3-56 zlibbioc_1.38.0 Rtsne_0.15 rhdf5_2.36.0 plyr_1.8.7
[71] grid_4.1.0 LiblineaR_2.10-12 parallel_4.1.0 listenv_0.8.0 crayon_1.5.1
[76] lattice_0.20-45 Biostrings_2.60.2 splines_4.1.0 multtest_2.48.0 hms_1.1.1
[81] beanplot_1.2 pillar_1.7.0 igraph_1.2.11 uuid_1.0-4 boot_1.3-28
[86] reshape2_1.4.4 codetools_0.2-18 stats4_4.1.0 glue_1.6.2 data.table_1.14.2
[91] nloptr_2.0.0 vctrs_0.3.8 foreach_1.5.2 tidyr_1.2.0 gtable_0.3.0
[96] purrr_0.3.4 future_1.24.0 assertthat_0.2.1 gridBase_0.4-7 survival_3.3-1
[101] tibble_3.1.6 lmerTest_3.1-3 iterators_1.0.14 IRanges_2.26.0 cluster_2.1.2
[106] corrplot_0.92 globals_0.14.0 ellipsis_0.3.2

[jakob-wirbel]

Hi @borexino

I think your error comes from a typo in the code:

label.meta <- - create.label(meta=meta,
                             label="Sex", case="female") 

This line has a - too much :)

It should be:

label.meta <- create.label(meta=meta,
                             label="Sex", case="female") 

The function seems to work well since the message said that the function was finished :D

However, since you are starting from a phyloseq, you can just create a SIAMCAT object from it directly:

sc.obj <- siamcat(phyloseq= pseq_genus, label='Sex', case='female')

This should work better :)

Cheers Jakob

[borexino]

No incredible! I was going crazy for this! Sorry and Thx!