msTab-M sample metadata information

The mtd_samples() function aids in creating and formatting the (optional) sample information from the mzTab-M metadata section. If defined, the sample information must be correctly linked to from the assay section. In particular, the assays need to link to the index of the samples defined in this section. One entry for each originating sample should be defined (without information on experimental properties). For each sample one or more additional characteristics (such as species, tissue, cell_type or disease) can be provided. Thus, these parameters expect the input be provided as a list. In addition, if a single value needs to be assigned to each sample, a character(1) of length 1 can be provided with the respective input parameter.

Important: to support the optional additional parameters passed along with ... all parameters (such as sample, species etc) have to be fully spelled out.

For details and expected input for the various parameter it is strongly suggested to consult the mzTab-M documentation.

Usage

mtd_sample(
  ...,
  sample = character(),
  species = list(),
  tissue = list(),
  cell_type = list(),
  disease = list(),
  description = character()
)

Arguments

...: optional custom information for each individual sample. Each custom variable is expected to be provided as a character of length equal to the length of parameter sample.
sample: character with the labels/names of the individual samples.
species: list of length equal to length(sample) with each element providing the species (eventually multiple) for each sample. Can also be a character of length(sample) to assing a single species to each sample, or a character(1) of length one to assign the same species to every sample.
tissue: list with the tissue(s) of each sample. The same format as described for parameter species can be used.
cell_type: list with the cell type(s) of each sample. The same format as described for parameter species can be used.
disease: list with the disease(s) of each sample. The same format as described for parameter species can be used.
description: character of length equal to length(sample) with optional description of each sample.

Value

two column character matrix with the information formatted as sample section of the mzTab-M format.

Examples


## Example sample description data.frame for an experiment
pd <- data.frame(
    sample_name = c("ind_1", "ind_2", "ind_1", "ind_2"),
    sample_id = c("i1_t1", "i2_t2", "i1_t2", "i2_t2"),
    time_point = c(1, 2, 1, 2))

## Define a minimal sample information with just the sample names.
mtd_sample(unique(pd$sample_name))
#>      [,1] [,2]

## Add also species information: each sample from the same species
mtd_sample(
    sample = unique(pd$sample_name),
    species = "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]")
#> 0
#>                                                                          
#> [1,] "sample[1]"            "ind_1"                                      
#> [2,] "sample[1]-species[1]" "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"
#> [3,] "sample[2]"            "ind_2"                                      
#> [4,] "sample[2]-species[1]" "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"

## Assume first sample is a mixture of two species
mtd_sample(
    sample = unique(pd$sample_name),
    species = list(c("[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]",
                     "[NCBITaxon, NCBITaxon:39767, Human rhinovirus 11, ]"),
                   "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]")
)
#> 0
#>                            
#> [1,] "sample[1]"           
#> [2,] "sample[1]-species[1]"
#> [3,] "sample[1]-species[2]"
#> [4,] "sample[2]"           
#> [5,] "sample[2]-species[1]"
#>                                                           
#> [1,] "ind_1"                                              
#> [2,] "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"        
#> [3,] "[NCBITaxon, NCBITaxon:39767, Human rhinovirus 11, ]"
#> [4,] "ind_2"                                              
#> [5,] "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"        

## Add full information including tissue, cell type and disease
mtd_sample(
    sample = unique(pd$sample_name),
    species = list(c("[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]",
                     "[NCBITaxon, NCBITaxon:39767, Human rhinovirus 11, ]"),
                   "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"),
    tissue = "[BTO, BTO:0000759, liver, ]",
    cell_type = "[CL, CL:0000182, hepatocyte, ]",
    disease = list(c("[DOID, DOID:684, hepatocellular carcinoma, ]",
                     "[DOID, DOID:9451, alcoholic fatty liver, ]"),
                   NULL)
)
#> 0
#>                               
#>  [1,] "sample[1]"             
#>  [2,] "sample[1]-species[1]"  
#>  [3,] "sample[1]-species[2]"  
#>  [4,] "sample[1]-tissue[1]"   
#>  [5,] "sample[1]-cell_type[1]"
#>  [6,] "sample[1]-disease[1]"  
#>  [7,] "sample[1]-disease[2]"  
#>  [8,] "sample[2]"             
#>  [9,] "sample[2]-species[1]"  
#> [10,] "sample[2]-tissue[1]"   
#> [11,] "sample[2]-cell_type[1]"
#>                                                            
#>  [1,] "ind_1"                                              
#>  [2,] "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"        
#>  [3,] "[NCBITaxon, NCBITaxon:39767, Human rhinovirus 11, ]"
#>  [4,] "[BTO, BTO:0000759, liver, ]"                        
#>  [5,] "[CL, CL:0000182, hepatocyte, ]"                     
#>  [6,] "[DOID, DOID:684, hepatocellular carcinoma, ]"       
#>  [7,] "[DOID, DOID:9451, alcoholic fatty liver, ]"         
#>  [8,] "ind_2"                                              
#>  [9,] "[NCBITaxon, NCBITaxon:9606, Homo sapiens, ]"        
#> [10,] "[BTO, BTO:0000759, liver, ]"                        
#> [11,] "[CL, CL:0000182, hepatocyte, ]"                     

## Add also additional custom variables
mtd_sample(sample = c("A", "B"),
    c("[,,Extraction date, 2011-12-21]",
      "[,,Extraction date, 2011-12-22]"),
    c("[,,Extraction reason, liver biopsy]",
      "[,,Extraction reason, liver biopsy]"))
#> 2
#>                                                                 
#> [1,] "sample[1]"           "A"                                  
#> [2,] "sample[1]-custom[1]" "[,,Extraction date, 2011-12-21]"    
#> [3,] "sample[1]-custom[2]" "[,,Extraction reason, liver biopsy]"
#> [4,] "sample[2]"           "B"                                  
#> [5,] "sample[2]-custom[1]" "[,,Extraction date, 2011-12-22]"    
#> [6,] "sample[2]-custom[2]" "[,,Extraction reason, liver biopsy]"

Usage

Arguments

Value

See also

Examples