Package 'rtemis.bio'

Title: rtemis Bio-informatics
Description: Bio-informatics utilities extending rtemis package.
Authors: E.D. Gennatas [aut, cre] (ORCID: <https://orcid.org/0000-0001-9280-3609>)
Maintainer: E.D. Gennatas <[email protected]>
License: GPL (>= 3)
Version: 0.4.2
Built: 2026-05-13 00:20:31 UTC
Source: https://github.com/rtemis-org/rtemis.bio

Help Index

rtemis.bio: Bioinformatics ops

Description

Bioinformatics utilities

Author(s)

Maintainer: E.D. Gennatas [email protected] (ORCID)

See Also

Useful links:

Perform amino acid substitutions

Description

Perform amino acid substitutions

Usage

aa_sub(x, substitutions, verbosity = 1L)

Arguments

x

Character vector: Amino acid sequence. e.g. "ARND" or c("A", "R", "N", "D").
substitutions

Character vector: Substitutions to perform in the format "OriginalPositionNew", e.g. c("C291A", "C322A").
verbosity

Integer: Verbosity level.

Value

Character vector with substitutions performed.

Author(s)

EDG

Aggregate method for Xt object

Description

Aggregate method for Xt object

Usage

## S3 method for class 'Xt'
aggregate(
  x,
  groupname,
  fn = mean,
  backend = getOption("rtemis_backend", "base"),
  ...
)

Arguments

x

Xt object.
groupname

Character: Grouping variable.
fn

Function: Function to apply to each group.
backend

Character: "base", "data.table", or "dplyr"; backend to use for aggregation.
...

Additional arguments passed to fn.

Author(s)

EDG

as_A3

Description

as_A3

Usage

as_A3(x)

Arguments

x

List: Named list with elements Sequence, Annotations, UniprotID. Annotations is a named list with possible elements Site, Region, PTM, Cleavage_site, Variant, Description, Reference.

Value

A3 object.

Author(s)

EDG

as_Xt

Description

as_Xt

Usage

as_Xt(x)

Arguments

x

Object to convert to Xt.

Value

Xt object.

Author(s)

EDG

Create an A3 object

Description

Creates an A3 object given amino acid sequence and annotations.

Usage

create_A3(
  sequence,
  site = NULL,
  region = NULL,
  ptm = NULL,
  cleavage_site = NULL,
  variant = NULL,
  uniprotid = NULL,
  description = NULL,
  reference = NULL
)

Arguments

sequence

Character: Amino acid sequence.
site

Named list of vectors of integer indices of sites, e.g. list("N-terminal repeat" = c(46, 47, 52), "Microtubule binding domain" = c(244, 245, 246))
region

Named list of integer indices, e.g. list("Phosphodegron" = c(46, 47, 48, 49, 50, 51), "KXGS" = c(259, 260, 261, 262)) or character vectors with index range of regions in format start:end, e.g. list(Phosphodegron = c("46:51", "149:154"), KXGS = c("259:262", "290:293"))
ptm

Named list of vectors with indices of post-translational modifications, e.g. list("Phosphorylation" = c(17, 18, 29, 30), "Acetylation" = c(148, 150, 163))
cleavage_site

Named list of cleavage sites, e.g. list(CTSL = c(54, 244, 319), CTSD = c(340, 391, 426))
variant

List of lists with variant information. Each list must contain a position element.
uniprotid

Character: Uniprot ID.
description

Character: Description of the data / experiment.
reference

Character: Link to reference (journal publication, preprint, etc.)

Details

We choose to keep NULL elements as empty lists in JSON, since we want users to be able to easily add annotations, whether programmaticaly, using a web app, or manually.

Value

A3 object

Author(s)

EDG

Create an Xt object

Description

Creates an Xt object from time series data.

Usage

create_Xt(
  x,
  y,
  x2 = NULL,
  y2 = NULL,
  zt = NULL,
  shade = NULL,
  group = NULL,
  xunits = NULL,
  yunits = NULL,
  y2units = NULL,
  description = NULL,
  reference = NULL
)

Arguments

x

Named list of datetime vectors.
y

Named list of numeric vectors: When plotted, these will correspond to the left y-axis.
x2

Named list of datetime vectors: When plotted, these will correspond to the right x-axis. If not provided, x will be used for both y and y2.
y2

Named list of numeric vectors: When plotted, these will correspond to the right y-axis.
zt

Numeric vector: Zeitgeber time. If provided, this will be used to label x-axis ticks. Assumes a single datetime vector in x. Elements in zt must correspond to elements in x.
shade

Binary vector: 0 indicates no shading, 1 indicates shading. If provided, this will be used to shade the plot.
group

Named list of factors: Grouping variable(s).
xunits

Character: Units for x.
yunits

Character: Units for y.
y2units

Character: Units for y2.
description

Character: Description of the data / experiment.
reference

Character: Link to reference (journal publication, preprint, etc.)

Value

Xt object

Author(s)

EDG

Get the sequence of a gene

Description

Get the sequence of a gene

Usage

gene2sequence(
  gene,
  organism = "hsapiens",
  biomart = "ensembl",
  host = "https://www.ensembl.org",
  seq_type = "coding",
  verbosity = 1L
)

Arguments

gene

Character: Gene name.
organism

Character: Organism name.
biomart

Character: Biomart name.
host

Character: Host address.
seq_type

Character: Sequence type to retrieve. See biomaRt::getSequence.
verbosity

Integer: Verbosity level.

Value

data.frame with columns "gene", "ensembl_transcript_id" and "sequence".

Author(s)

EDG

Get AlphaFold info for a given UniProt ID

Description

Get AlphaFold info for a given UniProt ID

Usage

get_alphafold(uniprotid)

Arguments

uniprotid

Character: UniProt ID.

Value

data frame with AlphaFold info.

Author(s)

EDG

Calculate light/dark ratio for Xt object

Description

Calculates light/dark ratio for each y and y2 timeseries in an Xt object.

Usage

light_dark_ratio(
  x,
  groupname = "Lights",
  fn = mean,
  backend = getOption("rtemis_backend", "data.table"),
  ...
)

Arguments

x

Xt object.
groupname

Character: Grouping variable.
fn

Function: Function to apply to each group.
backend

Character: "base", "data.table", or "dplyr"; backend to use for aggregation.
...

Additional arguments passed to fn.

Value

data.frame with columns for group and summary statistic.

Author(s)

EDG

Plot method for A3 object

Description

Plot method for A3 object

Usage

## S3 method for class 'A3'
plot(x, ...)

Arguments

x

A3 object.
...

Additional arguments passed to rtemis::draw_protein.

Value

plotly object.

Author(s)

EDG

Plot method for Xt object

Description

Plot method for Xt object

Usage

## S3 method for class 'Xt'
plot(x, ...)

Arguments

x

Xt object.
...

Additional arguments passed to rtemis::draw_xt.

Value

plotly object.

Author(s)

EDG

Read A3 object from JSON file

Description

Read A3 object from JSON file

Usage

read_A3json(filepath, verbosity = 0L)

Arguments

filepath

Character: Path to JSON file.
verbosity

Integer: if greater than 0, print messages.

Value

A3 object.

Author(s)

EDG

Read Xt object from JSON file

Description

Read Xt object from JSON file

Usage

read_Xtjson(filepath, verbosity = 0L)

Arguments

filepath

Character: Path to JSON file.
verbosity

Integer: if greater than 0, print messages.

Details

Note that factors saved under group are written as character by write_Xtjson and when they are read back in, they are converted back to factors using factor. This means that the levels will be set alphabetically. If needed, reorder them after reading in the JSON file using factor.

Value

Xt object.

Author(s)

EDG

Summary method for A3 object

Description

Summary method for A3 object

Usage

## S3 method for class 'A3'
summary(object, ...)

Arguments

object

A3 object.
...

Not used

Value

Called for side effects, prints summary to console.

Author(s)

EDG

Get protein sequence from UniProt

Description

Get protein sequence from UniProt

Usage

uniprot_get(
  accession,
  baseURL = "https://rest.uniprot.org/uniprotkb",
  verbosity = 1L
)

Arguments

accession

Character: UniProt Accession number - e.g. "Q9UMX9".
baseURL

Character: UniProt rest API base URL.
verbosity

Integer: Verbosity level.

Value

List with three elements: Identifier, Annotation, and Sequence.

Author(s)

E.D. Gennatas

Examples

## Not run: 
mapt <- uniprot_get("Q9UMX9")

## End(Not run)

Write A3 object to JSON file

Description

Write A3 object to JSON file

Usage

write_A3json(x, filepath, overwrite = FALSE)

Arguments

x

A3 object, as created by as_A3().
filepath

Character: Path to save JSON file.
overwrite

Logical: If TRUE, overwrite existing file.

Value

Nothing. Writes JSON file.

Author(s)

EDG

Write Xt object to JSON file

Description

Write Xt object to JSON file

Usage

write_Xtjson(x, filepath, overwrite = FALSE)

Arguments

x

Xt object, as created by as_Xt.
filepath

Character: Path to save JSON file.
overwrite

Logical: If TRUE, overwrite existing file.

Value

Nothing. Writes JSON file.

Author(s)

EDG