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Merge samples by a sample variable or factor

Source: R/speedyseq_functions.R
merge_samples2.Rd

lifecycle-stable

Firstly release in the speedyseq R package by Michael R. McLaren.

This function provides an alternative to phyloseq::merge_samples() that better handles sample variables of different types, especially categorical sample variables. It combines the samples in x defined by the sample variable or factor group by summing the abundances in otu_table(x) and combines sample variables by the summary functions in funs. The default summary function, unique_or_na(), collapses the values within a group to a single unique value if it exists and otherwise returns NA. The new (merged) samples are named by the values in group.

Usage

merge_samples2(
  x,
  group,
  fun_otu = sum,
  funs = list(),
  reorder = FALSE,
  default_fun = unique_or_na
)

# S4 method for class 'phyloseq'
merge_samples2(
  x,
  group,
  fun_otu = sum,
  funs = list(),
  reorder = FALSE,
  default_fun = unique_or_na
)

# S4 method for class 'otu_table'
merge_samples2(
  x,
  group,
  fun_otu = sum,
  reorder = FALSE,
  default_fun = unique_or_na
)

# S4 method for class 'sample_data'
merge_samples2(
  x,
  group,
  funs = list(),
  reorder = FALSE,
  default_fun = unique_or_na
)

Arguments

x

A phyloseq, otu_table, or sample_data object

group

A sample variable or a vector of length nsamples(x) defining the sample grouping. A vector must be supplied if x is an otu_table

fun_otu

Function for combining abundances in the otu_table; default is sum. Can be a formula to be converted to a function by purrr::as_mapper()

funs

Named list of merge functions for sample variables; default is unique_or_na

reorder

Logical specifying whether to reorder the new (merged) samples by name

default_fun

Default functions if funs is not set. Per default the function unique_or_na is used. See diff_fct_diff_class() for a useful alternative.

Value

A new phyloseq-class, otu_table or sam_data object depending on the class of the x param

Author

Michael R. McLaren (orcid: 0000-0003-1575-473X) modified by Adrien Taudiere

Examples

data(enterotype)

# Merge samples with the same project and clinical status
ps <- enterotype
sample_data(ps) <- sample_data(ps) %>%
  transform(Project.ClinicalStatus = Project:ClinicalStatus)
sample_data(ps) %>% head()
#>           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 Project.ClinicalStatus
#> AM.AD.1    28        healthy         gill06:healthy
#> AM.AD.2    37        healthy         gill06:healthy
#> AM.F10.T1  NA          obese      turnbaugh09:obese
#> AM.F10.T2  NA          obese      turnbaugh09:obese
#> DA.AD.1    59        healthy        MetaHIT:healthy
#> DA.AD.1T   NA           <NA>                   <NA>
ps0 <- merge_samples2(ps, "Project.ClinicalStatus",
  fun_otu = mean,
  funs = list(Age = mean)
)
#> Warning: `group` has missing values; corresponding samples will be dropped
sample_data(ps0) %>% head()
#>                     Enterotype Sample_ID SeqTech SampleID     Project
#> gill06:healthy            <NA>      <NA>  Sanger     <NA>      gill06
#> kurokawa07:healthy        <NA>      <NA>  Sanger     <NA>  kurokawa07
#> kurokawa07 :healthy       <NA>      <NA>  Sanger     <NA> kurokawa07 
#> MetaHIT:CD                   1   ES.AD.1  Sanger  ES.AD.1     MetaHIT
#> MetaHIT:healthy           <NA>      <NA>  Sanger     <NA>     MetaHIT
#> MetaHIT:obese             <NA>      <NA>  Sanger     <NA>     MetaHIT
#>                     Nationality Gender      Age ClinicalStatus
#> gill06:healthy         american   <NA> 32.50000        healthy
#> kurokawa07:healthy     japanese      M 15.12500        healthy
#> kurokawa07 :healthy    japanese   <NA> 19.17364        healthy
#> MetaHIT:CD              spanish      F 25.00000             CD
#> MetaHIT:healthy            <NA>   <NA> 50.00000        healthy
#> MetaHIT:obese            danish   <NA> 54.00000          obese
#>                     Project.ClinicalStatus
#> gill06:healthy              gill06:healthy
#> kurokawa07:healthy      kurokawa07:healthy
#> kurokawa07 :healthy    kurokawa07 :healthy
#> MetaHIT:CD                      MetaHIT:CD
#> MetaHIT:healthy            MetaHIT:healthy
#> MetaHIT:obese                MetaHIT:obese