Reading Portable Encapsulated Projects

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Documentation for package ‘pepr’ version 0.4.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

$-method	Access '"Config"' object elements
.appendAttrs	Append constant attributes across all the samples
.applyAmendments	Apply amendments
.applyImports	Function for recursive config data imports
.checkSection	Check for a section existence in a nested list
.deriveAttrs	Derive attributes
.duplicateAttrs	Duplicate a selected attribute across all the samples
.expandList	Recursively try to expand list of strings
.expandPath	Expand system path
.getSubscript	Get list subscript
.implyAttrs	Imply attributes
.inferProjectName	Infer project name
.isAbsolute	Determine whether a path is absolute.
.listifyDF	Listify data frame columns
.loadConfig	Load the config of a PEP
.loadSampleAnnotation	Read sample annotation from disk
.loadSubsampleAnnotation	Load single subsample annotation
.makeAbsPath	Create an absolute path from a primary target and a parent candidate.
.matchesAndRegexes	Create a list of matched files in the system and unmatched regular expessions
.mergeAttrs	Merge samples defined in sample table with ones in subsample table(s)
.modifySamples	Perform all the sample addribute modifications
.printNestedList	Print a nested list
.reformat	Check config spec version and reformat if needed
.removeAttrs	Remove attributes across all the samples
.strformat	Format a string like python's format method
activateAmendments	Activate amendments in objects of '"Project"'
activateAmendments-method	Activate amendments in objects of '"Project"'
checkSection	Check for existence of a section in the Project config
checkSection-method	Check for existence of a section in the Project config
Config	Config objects and specialized list obejcts and expand string attributes
config	Extract '"Project"'
Config-class	Config objects and specialized list obejcts and expand string attributes
config-method	Extract '"Project"'
fetchSamples	Collect samples fulfilling the specified requirements
getSample	Extract samples
getSample-method	Extract samples
getSubsample	Extract samples
getSubsample-method	Extract samples
listAmendments	List amendments
listAmendments-method	List amendments
makeSectionsAbsolute	Make selected sections absolute using config path
makeSectionsAbsolute-method	Make selected sections absolute using config path
pepr	pepr
Project	The constructor of a class representing a Portable Encapsulated Project
Project-class	Portable Encapsulated Project object
sampleTable	View samples in the objects of '"Project"'
sampleTable-method	View samples in the objects of '"Project"'
select-config	Access '"Config"' object elements
[-method	Access '"Config"' object elements
[[-method	Access '"Config"' object elements