Package 'pepr'

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

.Object	an object of class "Project"
amendments	character with the amendment name

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

object	object of "Config"
sectionNames	the name of the section or names of the nested sections to look for

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

object

an object of "Project"

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)

---

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

file	a character with project configuration yaml file
amendments	a character with the amendments names to be activated

Value

an object of "Config" class

Examples

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

---

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

samples	an object of data.table-class class
attr	a string specifying a column in the samples
func	an anonymous function, see Details for more information
action	a string (either include or exclude) that specifies whether the function should select the row or exclude it.

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

.Object	An object of Project class
sampleName	character the name of the sample

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

.Object	An object of Project class
sampleName	character the name of the sample
subsampleName	character the name of the subsample

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

.Object

an object of "Project"

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

object	"Config"
sections	character set of sections to make absolute
cfgPath	character absolute path to the config YAML file

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/

---

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

file	a string specifying a path to a project configuration YAML file
amendments	a string with the amendments names to be activated
sampleTableIndex	a string indicating the sample attribute that is used to index the sample table
subSampleTableIndex	a string indicating the sample attribute that is used to index the sample table

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

---

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

object

an object of "Project"

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

x	a "Config" object.
i	position of the identifier or the name of the identifier itself.
name	name of the element to access.

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

---