Package 'mgi.report.reader'

Description

chromosomes() returns mouse chromosome names.

Usage

chromosomes(autosomal = TRUE, sexual = TRUE, mitochondrial = TRUE)

Arguments

Value

A character vector of mouse chromosome names, or a subset thereof, or an empty character vector.

Examples

# All chromosomes.
chromosomes()

# Autosomal chromosomes.
chromosomes(autosomal = TRUE, sexual = FALSE, mitochondrial = FALSE)

Description

A dataset containing different types of gene and genome features along with their Sequence Ontology (SO) identifiers and definitions.

Usage

feature_type_definitions

Format

A tibble with 71 rows and 3 variables:

feature_type

Character. The type of gene or genome feature.

so_id

Character. The Sequence Ontology identifier associated with the feature type.

definition

Character. The definition of the feature type.

Source

The table in https://www.informatics.jax.org/userhelp/GENE_feature_types_help.shtml and a few other terms found in MGI reports.

Examples

print(feature_type_definitions, n = Inf)

Description

feature_types() returns different types of gene and genome features. For feature type definitions, see ?feature_type_definitions.

Usage

feature_types()

Value

A character vector of feature types' names.

Examples

feature_types()

Description

A dataset of marker types definitions.

Use instead marker_types() for the marker type names as a single character vector.

Usage

marker_type_definitions

Format

A tibble with 10 rows and 2 variables:

marker_type

Character. The type of genetic marker.

definition

Character. The definition of the marker type.

Source

The cross-references in the entry definition for marker at MGI glossary: https://www.informatics.jax.org/glossary/marker/.

Examples

print(marker_type_definitions, n = Inf)

Description

marker_types() returns MGI marker types. See marker_type_definitions for the meaning of each type.

Usage

marker_types()

Value

A character vector.

Examples

marker_types()

Description

open_marker_id_in_mgi() launches the web browser and opens a tab for each MGI accession identifier on the Mouse Genome Informatics web interface: https://www.informatics.jax.org.

Usage

open_marker_id_in_mgi(marker_id)

Arguments

Value

Returns TRUE if successful, or FALSE otherwise. But note that this function is run for its side effect of launching the browser.

Examples

# Read about Acta1 (actin alpha 1, skeletal muscle) online.
open_marker_id_in_mgi("MGI:87902")

# `open_marker_id_in_mgi()` is vectorized, so you can open multiple pages.
# NB: think twice if you really need to open many tabs at once.
open_marker_id_in_mgi(c("MGI:87902", "MGI:87909"))

Description

open_marker_symbol_in_mgi() launches the web browser and opens a tab for each MGI symbol on the Mouse Genome Informatics web interface: https://www.informatics.jax.org.

Usage

open_marker_symbol_in_mgi(marker_symbol)

Arguments

Value

Returns TRUE if successful, or FALSE otherwise. But note that this function is run for its side effect of launching the browser.

Examples

# Read about Acta1 (actin alpha 1, skeletal muscle) online.
open_marker_symbol_in_mgi("Acta1")

# `open_marker_symbol_in_mgi()` is vectorized, so you can open multiple pages.
# NB: think twice if you really need to open many tabs at once.
open_marker_symbol_in_mgi(c("Acta1", "Hes1"))

Description

read_report() imports data from an MGI report into R as a tidy data set.

You may call this function in two alternative ways:

• Using report_key: this is the easiest approach. A report key maps to a report currently hosted at MGI, e.g. read_report("marker_list2") reads MRK_List2.rpt directly from MGI server into R. See Supported Reports below for options.

• Using report_file and report_type: this approach is more flexible as you can read directly from a file or URL.

Supported Reports

The set of currently supported reports:

reports
#> # A tibble: 13 x 4
#>    report_key                 report_file              report_type   report_name
#>    <chr>                      <chr>                    <chr>         <chr>      
#>  1 marker_list1               MRK_List1.rpt            MRK_List1     Mouse Gene~
#>  2 marker_list2               MRK_List2.rpt            MRK_List2     Mouse Gene~
#>  3 marker_coordinates         MGI_MRK_Coord.rpt        MGI_MRK_Coord MGI Marker~
#>  4 gene_model_coordinates     MGI_Gene_Model_Coord.rpt MGI_Gene_Mod~ MGI Gene M~
#>  5 sequence_coordinates       MGI_GTGUP.gff            MGI_GTGUP     MGI Sequen~
#>  6 genbank_refseq_ensembl_ids MRK_Sequence.rpt         MRK_Sequence  MGI Marker~
#>  7 swiss_trembl_ids           MRK_SwissProt_TrEMBL.rpt MRK_SwissPro~ MGI Marker~
#>  8 swiss_prot_ids             MRK_SwissProt.rpt        MRK_SwissProt MGI Marker~
#>  9 gene_trap_ids              MRK_GeneTrap.rpt         MRK_GeneTrap  MGI Marker~
#> 10 ensembl_ids                MRK_ENSEMBL.rpt          MRK_ENSEMBL   MGI Marker~
#> 11 biotype_conflicts          MGI_BioTypeConflict.rpt  MGI_BioTypeC~ MGI Marker~
#> 12 primers                    PRB_PrimerSeq.rpt        PRB_PrimerSeq MGI Marker~
#> 13 interpro_domains           MGI_InterProDomains.rpt  MGI_InterPro~ InterPro d~

Usage

read_report(
  report_key = NULL,
  report_file = NULL,
  report_type = NULL,
  n_max = Inf
)

Arguments

Value

A tibble with report data in tidy format. The set of variables is dependent on the specific report requested:

• For "marker_list1", see vignette("marker_list1").

• For "marker_list2", see vignette("marker_list2").

• For "marker_coordinates", see vignette("marker_coordinates").

• For "gene_model_coordinates", see vignette("gene_model_coordinates").

• For "sequence_coordinates", see vignette("sequence_coordinates").

• For "genbank_refseq_ensembl_ids", see vignette("genbank_refseq_ensembl_ids").

• For "swiss_trembl_ids", see vignette("swiss_trembl_ids").

• For "swiss_prot_ids", see vignette("swiss_prot_ids").

• For "gene_trap_ids", see vignette("gene_trap_ids").

• For "ensembl_ids", see vignette("ensembl_ids").

• For "biotype_conflicts", see vignette("biotype_conflicts").

• For "primers", see vignette("primers").

• For "interpro_domains", see vignette("interpro_domains").

Description

report_example() returns the local path of an example report file. These files are typically very small and are useful for demonstrations. These are mostly used in the Examples section of functions and in unit tests.

Usage

report_example(report_file)

Arguments

Examples

report_example("MRK_List1-EX01.rpt")

report_example("MRK_List1-EX02.rpt")

report_example("MRK_List1-EX03.rpt")

Description

report_last_modified() returns the last modified date and time of the report source: local file or remote file. If a local file, the modification date will be that indicated by the file system; if a remote file, the date of last update is that provided by HTTP header "last-modified".

MGI updates its reports weekly, every Thursday. However, not all reports are updated each week. The return value of this function is the closest you will get to a versioning of MGI report files.

Usage

report_last_modified(tbl)

Arguments

Value

A last modified date-time as a POSIXct object.

Examples

if (FALSE) {
  markers <- read_report("marker_list1", n_max = 10L)

  # When was the report file last updated?
  report_last_modified(markers)
}

Description

report_source() returns the source used to obtain the report data: a file path or an URL.

Usage

report_source(tbl)

Arguments

Value

A single string with an absolute path to a file on disk or an URL.

Examples

if (FALSE) {
  markers <- read_report("marker_list1", n_max = 10L)

  # Where did the data come from?
  report_source(markers)
}

Description

Set of functions to retrieve metadata details of a MGI report.

Usage

report_file(report_key)

report_name(report_key)

report_type(report_key)

report_url(report_key)

Arguments

Value

A character vector:

• report_file(): report file name as hosted in https://www.informatics.jax.org/downloads/reports/.

• report_name(): report title.

• report_type(): report type.

• report_url(): report remote location.

Examples

report_file("marker_list1")

report_name("marker_list1")

report_type("marker_list1")

report_url("marker_list1")

Description

reports is a data set of supported MGI reports, meaning reports that {mgi.report.reader} can currently read into R. To browse all reports made available by MGI visit https://www.informatics.jax.org/downloads/reports/.

Usage

reports

Format

A tibble of 4 variables:

report_key

A string key used to uniquely refer to an MGI report, which is only meaningful within the context of the {mgi.report.reader}.

report_file

MGI report file name as hosted at https://www.informatics.jax.org/downloads/reports/.

report_type

MGI report type. The type is used internally to find the appropriate reader for parsing, and is only meaningful within the context of {mgi.report.reader}.

report_name

MGI report name. Report names are taken from https://www.informatics.jax.org/downloads/reports/index.html.

Examples

reports

Description

symbol_to_identifier() remaps old marker symbols to, in-use, most up to date marker identifiers.

Usage

symbol_to_identifier(x, report_file = NULL, n_max = Inf)

Arguments

Examples

rpt_ex01 <- report_example("MRK_List1-EX01.rpt")
read_report(report_file = rpt_ex01, report_type = "MRK_List1") |>
  dplyr::select("marker_status", "marker_symbol", "marker_id_now")

# NB:
#   - "1700024N20Rik" has two conflicting mappings, so maps to `NA`.
#   - "Hes1" is not present in MRK_List1-EX01.rpt, so maps to `NA`.
#   - "Plpbp" (official) and "Prosc" (withdrawn) both map to "MGI:1891207"

marker_symbols <- c("2200002F22Rik", "Plpbp", "Prosc", "1700024N20Rik", "Hes1")
symbol_to_identifier(x = marker_symbols, report_file = rpt_ex01)

Description

symbol_to_symbol() remaps old marker symbols to, in-use, most up to date symbols.

Usage

symbol_to_symbol(x, report_file = NULL, n_max = Inf)

Arguments

Value

A character vector of most up to date symbols.

Examples

rpt_ex01 <- report_example("MRK_List1-EX01.rpt")
read_report(report_file = rpt_ex01, report_type = "MRK_List1") |>
  dplyr::select("marker_status", "marker_symbol", "marker_symbol_now")

# NB:
#   - "1700024N20Rik" has two conflicting mappings, so maps to `NA`.
#   - "Hes1" is not present in MRK_List1-EX01.rpt, so maps to `NA`.
#   - "Plpbp" (official) and "Prosc" (withdrawn) both map to "Plpbp"

marker_symbols <- c("2200002F22Rik", "Plpbp", "Prosc", "1700024N20Rik", "Hes1")
symbol_to_symbol(x = marker_symbols, report_file = rpt_ex01)