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Add sequences, reports, trees or resource references to a strollur object

Source: R/add.R
add.Rd

Add sequences, reports, trees or resource references to a strollur object

Usage

add(
  data,
  table,
  type = "sequence",
  report_type = NULL,
  table_names = list(sequence_name = "sequence_name", sequence = "sequence", comment =
    "comment", quality_score = "quality_score", reference_vendor = "vendor",
    reference_name = "name", reference_version = "version", reference_usage = "usage",
    reference_note = "note", reference_method_url = "method_url",
    reference_documentation_url = "documentation_url", reference_parameter = "parameter",
    reference_citation = "citation"),
  reference = NULL,
  verbose = TRUE
)

Arguments

data

a strollur object

table

a data.frame or tree containing the data you wish to add.

type

a string containing the type of data. Options include: sequence, fastq, sample_tree, sequence_tree, resource_reference and report.

report_type

a string containing the type of report you are adding.

table_names

named list used to indicate the names of the columns in the table. By default:

table_names <- list(sequence_name = "sequence_name", comment = "comment", sequence = "sequence", quality_score = "quality_score", reference_name = "name", reference_vendor = "vendor", reference_version = "version", reference_usage = "usage", reference_note = "note", reference_documentation_url = "documentation_url", reference_method_url = "method_url", reference_parameter = "parameter", reference_citation = "citation")

In table_names, 'sequence_name' is a string containing the name of the column in 'table' that contains the sequence names. It is used when you are adding FASTA data. Default column name is 'sequence_name'.

In table_names, 'sequence' is a string containing the name of the column in 'table' that contains the sequence nucleotide strings. It is used when you are adding FASTA data. Default column name is 'sequence'.

In table_names, 'comment' is a string containing the name of the column in 'table' that contains the sequence comments. It is used when you are adding FASTA data. Default column name is 'comment'.

In table_names, 'quality_score' is a string containing the name of the column in 'table' that contains the sequence quality scores. It is used when you are adding FASTQ data. Default column name is 'quality_score'.

In table_names, 'reference_vendor' is a string containing the name of the column in 'table' that contains the reference vendor names. It is used when you are adding reference data. Default column name is 'vendor'. In table_names, 'reference_name' is a string containing the name of the column in 'table' that contains the reference names. It is used when you are adding reference data. Default column name is 'name'.

In table_names, 'reference_version' is a string containing the name of the column in 'table' that contains the reference versions. Default column name is 'version'.

In table_names, 'reference_usage' is a string containing the name of the column in 'table' that contains the reference usages. Default column name is 'usage'.

In table_names, 'reference_note' is a string containing the name of the column in 'table' that contains the reference notes. Default column name is 'note'.

In table_names, 'reference_method_url' is a string containing the name of the column in 'table' that contains the reference method urls. Default column name is 'method_url'.

In table_names, 'reference_documentation_url' is a string containing the name of the column in 'table' that contains the reference urls. Default column name is 'documentation_url'.

In table_names, 'reference_parameter' is a string containing the name of the column in 'table' that contains the reference parameters. Default column name is 'parameter'.

In table_names, 'reference_citation' is a string containing the name of the column in 'table' that contains the reference citations. Default column name is 'citation'.

reference

a list created by the function new_reference. Optional.

verbose

boolean indicating whether or not you want progress messages. Default = TRUE.

Value

an updated strollur object

Examples


# Create a new empty strollur object named 'example_dataset'
data <- strollur::new_dataset(dataset_name = "example_dataset")

# Read FASTA data into data.frame
fasta_data <-
  strollur::read_fasta(fasta = strollur_example("final.fasta.gz"))

# Add FASTA sequence data
strollur::add(data = data, table = fasta_data, type = "sequence")
#> Added 2425 sequences.

# To add FASTA data with a resource reference

# Create a new empty strollur object named 'example_dataset'
data <- strollur::new_dataset(dataset_name = "example_dataset")

# Create a resource reference for the FASTA data silva_resource <-
silva_resource <- strollur::new_reference(
  vendor = "SILVA", name =
    "silva.bacteria.fasta", version = "1.38.1",
  usage = "alignment of sequences",
  note = "reference trimmed to V4 region", method_url =
    "https://mothur.org/blog/2024/SILVA-v138_2-reference-files/",
  documentation_url = "https://mothur.org/wiki/silva_reference_files/"
)

# Add FASTA data with a resource reference

strollur::add(
  data,
  table = fasta_data,
  type = "sequence",
  reference = silva_resource
)
#> Added 2425 sequences.
#> Added 1 resource references.

# Create a new empty strollur object named 'example_dataset'
data <- strollur::new_dataset(dataset_name = "example_dataset")

# Read FASTQ data into data.frame
fastq_data <-
  strollur::read_fastq(fastq = strollur_example("tiny.fastq.gz"))

# Add FASTQ sequence data
strollur::add(data = data, table = fastq_data, type = "fastq")
#> Added 3 sequences.
#> Assigned 3 quality scores.

# Add contigs assembly report with a 'sequence_name' column named 'Name'

contigs_report <- readRDS(strollur_example("miseq_contigs_report.rds"))

strollur::add(
  data,
  table = contigs_report, type = "report",
  report_type = "contigs_report", list(sequence_name = "Name")
)
#> 
#> Your report does not contain an entry for every sequence in your dataset, ignoring report. 

# To add metadata related to your study

metadata <- readRDS(strollur_example("miseq_metadata.rds"))

strollur::add(data,
  table = metadata,
  type = "report", report_type = "metadata"
)
#> Added a metadata report.

# To add a tree relating to your sequences

tree <- ape::read.tree(strollur_example("final.phylip.tre.gz"))

strollur::add(data, table = tree, type = "sequence_tree")
#> → Your tree does not contain a node for every sequence in your dataset, ignoring tree. Missing tree nodes for: M00967:43:000000000-A3JHG:1:1101:18327:1699, M00967:43:000000000-A3JHG:1:1101:14069:1827, M00967:43:000000000-A3JHG:1:1101:18044:1900 .

# To add a tree relating to your samples
data <- strollur::new_dataset(dataset_name = "example_dataset")

df <- strollur::read_mothur_shared(strollur_example("final.opti_mcc.shared"))
tree <- ape::read.tree(strollur_example("final.opti_mcc.jclass.ave.tre"))

strollur::assign(data, table = df, type = "bin", bin_type = "otu")
#> Assigned 531 otu bins.
strollur::add(data, table = tree, type = "sample_tree")