Simple selection of phyloseq sample_data variables, might be useful for printing reduced sample_data, or inside other functions
ps_select(ps, ...)phyloseq with sample_data
passed straight to dplyr::select
phyloseq object
library(phyloseq)
library(dplyr)
data("enterotype", package = "phyloseq")
head(sample_data(enterotype))
#> Enterotype Sample_ID SeqTech SampleID Project Nationality Gender
#> AM.AD.1 <NA> AM.AD.1 Sanger AM.AD.1 gill06 american F
#> AM.AD.2 <NA> AM.AD.2 Sanger AM.AD.2 gill06 american M
#> AM.F10.T1 <NA> AM.F10.T1 Sanger AM.F10.T1 turnbaugh09 american F
#> AM.F10.T2 3 AM.F10.T2 Sanger AM.F10.T2 turnbaugh09 american F
#> DA.AD.1 2 DA.AD.1 Sanger DA.AD.1 MetaHIT danish F
#> DA.AD.1T <NA> DA.AD.1T Sanger <NA> <NA> <NA> <NA>
#> Age ClinicalStatus
#> AM.AD.1 28 healthy
#> AM.AD.2 37 healthy
#> AM.F10.T1 NA obese
#> AM.F10.T2 NA obese
#> DA.AD.1 59 healthy
#> DA.AD.1T NA <NA>
enterotype %>%
ps_select(!contains("Sample")) %>%
sample_data() %>%
head()
#> Enterotype SeqTech Project Nationality Gender Age ClinicalStatus
#> AM.AD.1 <NA> Sanger gill06 american F 28 healthy
#> AM.AD.2 <NA> Sanger gill06 american M 37 healthy
#> AM.F10.T1 <NA> Sanger turnbaugh09 american F NA obese
#> AM.F10.T2 3 Sanger turnbaugh09 american F NA obese
#> DA.AD.1 2 Sanger MetaHIT danish F 59 healthy
#> DA.AD.1T <NA> Sanger <NA> <NA> <NA> NA <NA>