Append constant attributes across all the samples

Description

Append constant attributes across all the samples

Usage

.appendAttrs(.Object)

Arguments

Value

an object of Project-class

Apply amendments

Description

Overwrite and/or add Project attributes from the amendments section

Usage

.applyAmendments(cfg, amendments = NULL)

Arguments

Value

possibly updated config

config

Function for recursive config data imports

Description

Function for recursive config data imports

Usage

.applyImports(cfg_data, filename)

Arguments

Value

config data enriched in imported sections, if imports existed in the input

Merge samples with identical names

Description

If sample table specifies samples with non-unique names, try to merge these samples

Usage

.autoMergeDuplicatedNames(.Object)

Arguments

Value

an object of "Project"

Check for a section existence in a nested list

Description

Check for a section existence in a nested list

Usage

.checkSection(object, sectionNames)

Arguments

Value

logical indicating whether the sections where found in the list

Examples

l = list(a=list(b="test"))
.checkSection(l,c("a","b"))
.checkSection(l,c("c","b"))

Derive attributes

Description

Derive attributes

Usage

.deriveAttrs(.Object)

Arguments

Value

an object of "Project"

Duplicate a selected attribute across all the samples

Description

Duplicate a selected attribute across all the samples

Usage

.duplicateAttrs(.Object)

Arguments

Value

an object of "Project"

Recursively try to expand list of strings

Description

Recursively try to expand list of strings

Usage

.expandList(x)

Arguments

Value

list of strings with paths expaned

Examples

x = list(a=list(b=list(c="~/test.txt")))
.expandList(x)

Expand system path

Description

This function expands system paths (the non-absolute paths become absolute) and replaces the environment variables (e.g, ${HOME}) with their values.

Usage

.expandPath(path)

Arguments

Details

Most importantly strings that are not system paths are returned untouched

Value

Expanded path or untouched string

Examples

string = "https://www.r-project.org/"
.expandPath(string)
path = "$HOME/my/path/string.txt"
.expandPath(path)

Get the sample table from config

Description

Get the sample table from config

Usage

.getSampleTablePathFromConfig(config)

Arguments

Value

a string which specifies a path to the sample table file

Get the subsample tables from config

Description

Get the subsample tables from config

Usage

.getSubSampleTablePathFromConfig(config)

Arguments

Value

string/vector of strings/NULL depending on the configuration

Get list subscript

Description

Based on available list element names and subscript value determine index of the element requested

Usage

.getSubscript(lst, i)

Arguments

Value

numeric index of the requested element in the list

Examples

l = list(a="a", b="b")
.getSubscript(l, 1) == .getSubscript(l, "a")

Set table indexes

Description

Get sample and subsample table indexes and save as a slot on the Project object

Usage

.getTableIndexes(.Object, stIndex, sstIndex)

Arguments

Details

This is the (sub)sample table index selection priority order:

1. Project constructor specified

2. Config specified

3. Deafult value

Imply attributes

Description

Imply attributes

Usage

.implyAttrs(.Object)

Arguments

Value

an object of "Project"

Infer project name

Description

Based on dedicated config section or PEP enclosing dir

Usage

.inferProjectName(cfg, filename)

Arguments

Value

string project name

Determine whether a path is absolute.

Description

Determine whether a path is absolute.

Usage

.isAbsolute(path)

Arguments

Value

Flag indicating whether the path appears to be absolute.

Config file or annotation file

Description

Determine if the input file seems to be a project config file (based on the file extension).

Usage

.isCfg(filePath)

Arguments

Value

a boolean, TRUE if indicating the path seems to be pointing to a config, or FALSE if the path seems to be pointing to an annotation file.

Determine whether the string is a valid URL

Description

Determine whether the string is a valid URL

Usage

.isValidUrl(str)

Arguments

Value

logical indicating whether a string is a valid URL

Listify data frame columns

Description

This function turns each data frame column into a list, so that its cells can contain multiple elements

Usage

.listifyDF(DF)

Arguments

Value

an object of class data.frame

Examples

dataFrame=mtcars
listifiedDataFrame=.listifyDF(dataFrame)

Load the config of a PEP

Description

Loads a PEP config file

Usage

.loadConfig(filename = NULL, amendments = NULL)

Arguments

See Also

https://pep.databio.org/

Read sample table from disk

Description

Read sample table from disk

Usage

.loadSampleAnnotation(sampleTablePath)

Arguments

Value

an data.frame with samples; one sample per row

Load single subsample annotation

Description

Load single subsample annotation

Usage

.loadSubsampleAnnotation(.Object, path)

Arguments

Value

an object of "Project"

Create an absolute path from a primary target and a parent candidate.

Description

Create an absolute path from a primary target and a parent candidate.

Usage

.makeAbsPath(perhapsRelative, parent)

Arguments

Value

Target itself if already absolute, else target nested within parent.

Create a list of matched files in the system and unmatched regular expessions

Description

Create a list of matched files in the system and unmatched regular expessions

Usage

.matchesAndRegexes(rgx)

Arguments

Value

a list of all the elements after possible expansion

Merge samples defined in sample table with ones in subsample table(s)

Description

Merge samples defined in sample table with ones in subsample table(s)

Usage

.mergeAttrs(.Object, subsampleAannotationPaths)

Arguments

Value

an object of "Project"

Perform all the sample attribute modifications

Description

Perform all the sample attribute modifications

Usage

.modifySamples(object)

Arguments

Value

modified Project object

Print a nested list

Description

Prints a nested list in a way that looks nice

Usage

.printNestedList(lst, level = 0)

Arguments

Details

Useful for displaying the config of a PEP

Value

No return value, called for side effects

Examples

projectConfig = system.file("extdata",
"example_peps-master",
"example_basic",
"project_config.yaml",
package = "pepr")
p = Project(file = projectConfig)
.printNestedList(config(p),level=2)

Check config spec version and reformat if needed

Description

Check config spec version and reformat if needed

Usage

.reformat(object)

Arguments

Value

an object of "Config"

Remove attributes across all the samples

Description

Remove attributes across all the samples

Usage

.removeAttrs(.Object)

Arguments

Value

an object of "Project"

Check whether the string is a valid URL or an existing local path

Description

Check whether the string is a valid URL or an existing local path

Usage

.safeFileExists(path)

Arguments

Value

a logical indicating whether it's an existing path or valid URL

Format a string like python's format method

Description

Given a string with environment variables (encoded like ${VAR} or $VAR), and other variables (encoded like {VAR}) this function will substitute both of these and return the formatted string, like the Python str.format() method. Other variables are populated from a list of arguments. Additionally, if the string is a non-absolute path, it will be expanded.

Usage

.strformat(string, args, parent = NULL)

Arguments

Value

Formatted string

Examples

.strformat("~/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))
.strformat("$HOME/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))

Config objects and specialized list obejcts and expand string attributes

Description

Config objects are used with the "Project" object

Usage

Config(file, amendments = NULL)

Arguments

Value

an object of "Config" class

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
c=Config(projectConfig)

The constructor of a class representing a Portable Encapsulated Project

Description

This is a helper that creates the project with empty samples and config slots

Usage

Project(
  file = NULL,
  amendments = NULL,
  sampleTableIndex = NULL,
  subSampleTableIndex = NULL
)

Arguments

Value

an object of "Project"

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p=Project(projectConfig)

Portable Encapsulated Project object

Description

Provides an in-memory representation and functions to access project configuration and sample annotation values for a PEP.

Details

Can be created with the constructor: "Project"

Slots

file

character vector path to config file on disk.

samples

a data table object holding the sample metadata

config

a list object holding contents of the config file

sampleNameAttr

a string indicating the sample attribute that is used to index the sample table

subSampleNameAttr

a string indicating the sample attribute that is used to index the sample table

Activate amendments in objects of "Project"

Description

This method switches between the amendments within the "Project" object

Usage

activateAmendments(.Object, amendments)

## S4 method for signature 'Project,character'
activateAmendments(.Object, amendments)

Arguments

Details

To check what are the amendments names call listAmendments(p), where p is the object of "Project" class

Value

an object of class "Project" with activated amendments

Methods (by class)

• activateAmendments(.Object = Project, amendments = character): activate amendments in a "Project" object

Examples

projectConfig = system.file("extdata",
"example_peps-master",
"example_amendments1",
"project_config.yaml",
package = "pepr")
p = Project(file = projectConfig)
availAmendments = listAmendments(p)
activateAmendments(p, availAmendments[1])

Check for existence of a section in the Project config

Description

This function checks for the section/nested sections in the config YAML file. Returns TRUE if it exist(s) or FALSE otherwise.

Usage

checkSection(object, sectionNames)

## S4 method for signature 'Config'
checkSection(object, sectionNames)

Arguments

Details

Element indices can be used instead of the actual names, see Examples.

Value

a logical indicating whether the section exists

Methods (by class)

• checkSection(Config): checks for existence of a section in "Config" objects

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p=Project(projectConfig)
checkSection(config(p),sectionNames = c("amendments","newLib"))
checkSection(config(p),sectionNames = c("amendments",1))

Extract "Project"

Description

This method can be used to view the config slot of the "Project" class

Usage

config(object)

## S4 method for signature 'Project'
config(object)

Arguments

Value

project config

Methods (by class)

• config(Project): Extract "Project" of the object of "Project"

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p=Project(projectConfig)
config(p)

Collect samples fulfilling the specified requirements

Description

This funciton collects the samples from a data.table-class object that fulfill the requirements of an attribute attr specified with the fun argument

Usage

fetchSamples(samples, attr = NULL, func = NULL, action = "include")

Arguments

Details

The anonymous function provided in the func argument has to return an integer that indicate the rows that the action should be performed on. Core expressions which are most useful to implement the anonymous function are:

• which with inequality signs: ==,>,<

• grep

Value

an object of data.table-class class filtered according to specified requirements

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p = Project(projectConfig)
s = sampleTable(p)
fetchSamples(s,attr = "sample_name", func=function(x){ which(x=="pig_0h") },action="include")
fetchSamples(s,attr = "sample_name", func=function(x){ which(x=="pig_0h") },action="exclude")
fetchSamples(s,attr = "sample_name", func=function(x){ grep("pig_",x) },action="include")

Extract samples

Description

This method extracts the samples

Usage

getSample(.Object, sampleName)

## S4 method for signature 'Project,character'
getSample(.Object, sampleName)

Arguments

Value

data.table one row data table with the sample associated metadata

Methods (by class)

• getSample(.Object = Project, sampleName = character): extracts the sample from the "Project" object

Examples

projectConfig = system.file(
"extdata",
"example_peps-master",
"example_basic",
"project_config.yaml",
package = "pepr"
)
p = Project(projectConfig)
sampleName = "frog_1"
getSample(p, sampleName)

Extract subsamples

Description

This method extracts the subsamples

Usage

getSubsample(.Object, sampleName, subsampleName)

## S4 method for signature 'Project,character,character'
getSubsample(.Object, sampleName, subsampleName)

Arguments

Value

data.table one row data table with the subsample associated metadata

Methods (by class)

• getSubsample( .Object = Project, sampleName = character, subsampleName = character ): extracts the subsamples from the "Project" object

Examples

projectConfig = system.file(
"extdata",
"example_peps-master",
"example_subtable1",
"project_config.yaml",
package = "pepr"
)
p = Project(projectConfig)
sampleName = "frog_1"
subsampleName = "sub_a"
getSubsample(p, sampleName, subsampleName)

List amendments

Description

Lists available amendments within a "Project" object.

Usage

listAmendments(.Object)

## S4 method for signature 'Project'
listAmendments(.Object)

Arguments

Details

The amendments can be activated by passing their names to the activateAmendments method

Value

names of the available amendments

Methods (by class)

• listAmendments(Project): list amendments in a "Project" object

Examples

projectConfig = system.file("extdata",
"example_peps-master",
"example_amendments1",
"project_config.yaml",
package = "pepr")
p = Project(file = projectConfig)
availAmendemtns = listAmendments(p)

Make selected sections absolute using config path

Description

Make selected sections absolute using config path

Usage

makeSectionsAbsolute(object, sections, cfgPath)

## S4 method for signature 'Config,character,character'
makeSectionsAbsolute(object, sections, cfgPath)

Arguments

Value

Config with selected sections made absolute

Methods (by class)

• makeSectionsAbsolute( object = Config, sections = character, cfgPath = character ): Make selected sections absolute using config path from "Project"

pepr

Description

Package documentation

Author(s)

Michal Stolarczyk, Nathan Sheffield

References

GitHub: https://github.com/pepkit/pepr, Documentation: https://code.databio.org/pepr/

View samples in the objects of "Project"

Description

This method can be used to view the samples slot of the "Project" class

Usage

sampleTable(object)

## S4 method for signature 'Project'
sampleTable(object)

Arguments

Value

a data.table with the with metadata about samples

Methods (by class)

• sampleTable(Project): extract sample table from a "Project"

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
p=Project(projectConfig)
sampleTable(p)

Access "Config" object elements

Description

You can subset Config by identifier or by position using the `[`, `[[` or `$` operator. The string will be expanded if it's a path.

Usage

## S4 method for signature 'Config'
x[i]

## S4 method for signature 'Config'
x[[i]]

## S4 method for signature 'Config'
x$name

Arguments

Value

An element held in "Config" object

Examples

projectConfig = system.file("extdata", "example_peps-master",
"example_amendments1", "project_config.yaml", package="pepr")
c=Config(projectConfig)
c[[2]]
c[2]
c[["sample_table"]]
c$sample_table