Package 'htce'

Retrieve a well_id from barcode and address strings

Description

Retrieve a well_id from barcode and address strings

Usage

address_to_well_id(
  barcode,
  address,
  .db_loc = "./htCE.duckdb",
  .db_con = NULL,
  .pg_load = FALSE
)

Arguments

barcode	A string - the unique barcode identifying the physical plate
address	A string - the well identifier (e.g. A1, H12, etc.)
.db_loc	A string - local path to the DuckDB file; passed to dkdb_collect()
.db_con	A valid DBIConnection object; passed to dkdb_collect()
.pg_load	A Boolean - use the DuckDB Postgres extension?; passed to dkdb_collect()

Value

A double value representing the well_id integer primary key which corresponds to the barcode and address arguments

---

Retrieve a plate_id from a barcode string

Description

Retrieve a plate_id from a barcode string

Usage

barcode_to_plate_id(
  barcode,
  .db_loc = "./htCE.duckdb",
  .db_con = NULL,
  .pg_load = FALSE
)

Arguments

barcode	A string - the unique barcode identifying the physical plate
.db_loc	A string - local path to the DuckDB file; passed to dkdb_collect()
.db_con	A valid DBIConnection object; passed to dkdb_collect()
.pg_load	A Boolean - use the DuckDB Postgres extension?; passed to dkdb_collect()

Value

A double value representing the plate_id integer primary key which corresponds to the barcode argument

---

Return the number of lines in a file

Description

Return the number of lines in a file

Usage

count_newlines(path, remove_header = TRUE, ignore_trailing = TRUE)

Arguments

path	A string - path to file
remove_header	A Boolean - should the first row be ignored?
ignore_trailing	A Boolean - should a trailing '\n' be ignored?

Value

An integer - the number of lines in the file

---

DuckDB Query

Description

Execute or collect results from a query to a DuckDB database.

Usage

dkdb_execute(
  query_string,
  ...,
  .quiet = TRUE,
  .db_loc = "./htCE.duckdb",
  .db_con = NULL,
  .pg_install = FALSE,
  .pg_load = FALSE
)

dkdb_collect(
  query_string,
  ...,
  .quiet = TRUE,
  .db_loc = "./htCE.duckdb",
  .db_con = NULL,
  .pg_install = FALSE,
  .pg_load = FALSE,
  .return = NULL
)

Arguments

query_string	A string - SQL query
...	Key-value pairs - additional injected values passed to glue::glue_sql()
.quiet	A Boolean - suppress console messages?
.db_loc	A string - local path to the DuckDB file
.db_con	A valid DBIConnection object
.pg_install	A Boolean - install the DuckDB Postgres extension?
.pg_load	A Boolean - use the DuckDB Postgres extension?
.return	A string - how collected data should be returned, default is a data.frame (alias df, see DBI::dbGetQuery()), but can also be coerced to a tibble (alias tbl, see tibble::as_tibble()) or data.table (alias dt, see data.table::as.data.table())

Details

dkdb_execute executes a query without collecting results.

dkdb_collect collects the results from a query and returns them as a tibble.

Value

A data.frame (default), tibble, or data.table containing the collected query results

---

Lookup something by a set of attributes and return the id or a Boolean value indicating if it already exists

Description

Lookup something by a set of attributes and return the id or a Boolean value indicating if it already exists

Usage

dkdb_lookup(
  ...,
  .table = NULL,
  .return = "id",
  .db_loc = "./htCE.duckdb",
  .db_con = NULL,
  .pg_load = FALSE
)

Arguments

...	Key-value pairs - unique set of injected arguments (using glue::glue_sql()) for component lookup
.table	A string - the table to query in the database schema
.return	A string - should the returned value be a component_id ("id") or a Boolean from an EXISTS operator subquery ("exists")
.db_loc	A string - local path to the DuckDB file; passed to dkdb_collect()
.db_con	A valid DBIConnection object; passed to dkdb_collect()
.pg_load	A Boolean - use the DuckDB Postgres extension?; passed to dkdb_collect()

Value

A primary key id as a double (.return = "id") or a Boolean value returned from an EXISTS operator subquery (.return = "exixts")

---

Title

Description

Title

Usage

existing_barcodes(
  source_only = FALSE,
  .table = "plates",
  .db_loc = "./htCE.duckdb",
  .db_con = NULL
)

Arguments

source_only	A Boolean - only retrieve source plate barcodes
.table	A string - the database table to query (⁠{.table}.barcode⁠)
.db_loc	A string - local path to the DuckDB file; passed to dkdb_collect()
.db_con	A valid DBIConnection object; passed to dkdb_collect()

Value

A named character vector of barcodes that exist in the database

---

Title

Description

Title

Usage

fatools_matrix(m)

Arguments

m

---

Find and return skip values

Description

Returns a named list of skip values for importing Echo transfer report metadata and transfer data.

Usage

find_skips(file_path)

Arguments

file_path

A string - the path to the .csv delimited file to read

Value

A named list of skip values to use during Echo transfer report import

---

Create CE submission files

Description

Creates tab-delimited files for submitting CE plates to the NEB sequencing core via the LIMS system.

Usage

make_submission_files(
  initials = "EH",
  datetime = NULL,
  plate_code = 5,
  num_wells = 96,
  num_plates = 12,
  dest_dir = NULL,
  .pad_well_num = FALSE
)

Arguments

initials	A string - your initials
datetime	A date - use base::as.Date to convert a string to a date
plate_code	An integer - a code representing the type of plate
num_wells	An integer - 96 or 384, the number of wells on the submission plate
num_plates	An integer - the number of plate submission files to create
dest_dir	A string - the directory to create the tab-delimited submission files
.pad_well_num	A Boolean - passed to make_well_order() pad argument

---

Create a vector of well addresses

Description

Create a vector of well addresses

Usage

make_well_order(num_wells, pad = FALSE)

Arguments

num_wells	An integer - the number of wells in the plate format (96 or 384)
pad	A Boolelan - whether or not to pad the column numbers with zeros (e.g. A1 vs. A01)

Value

A character vector of well addresses in top to bottom, left to right order (e.g. for 96 wells, A1 -> H1, A2...H11, A12 -> H12)

---

Title

Description

Title

Usage

new_fatools_matrix(m = matrix())

Arguments

m

---

Title

Description

Title

Usage

## S3 method for class 'fatools_matrix'
tidy(x, ...)

Arguments

x

---

Title

Description

Title

Usage

validate_fatools_matrix(m)

Arguments

m

---

DuckDB Connection

Description

DuckDB connection handling à la withr::local_db_connection.

Usage

with_duckdb_connection(
  db_file_path,
  read_only = FALSE,
  .local_envir = parent.frame()
)

Arguments

db_file_path	a string - path to a DuckDB file
read_only	a Boolean - passed to DBI::dbConnect(); default is FALSE
.local_envir	an environment - passed to withr::defer(); default is parent.frame()

Value

A database connection of class DBIConnection.

See Also

DBI::dbConnect(), withr::defer(), withr::local_db_connection(), duckdb/duckdb#5525

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