knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Learn derived attributes in pepr

This vignette will show you how and why to use the derived attributes functionality of the pepr package.

Problem/Goal

The example below demonstrates how to use the derived attributes to flexibly define the samples attributes the file_path column of the sample_table.csv file to match the file names in your project. Please consider the example below for reference:

branch = "master"
library(knitr)
sampleAnnotation = system.file(
"extdata",
paste0("example_peps-", branch),
"example_derived",
"sample_table_pre.csv",
package = "pepr"
)
sampleAnnotationDF = read.table(sampleAnnotation, sep = ",", header = T)
knitr::kable(sampleAnnotationDF, format = "html") 

Solution

As the name suggests the attributes in the specified attributes (here: file_path) can be derived from other ones. The way how this process is carried out is indicated explicitly in the project_config.yaml file (presented below). The name of the column is determined in the derived_attributes key-value pair, whereas the pattern for the attributes construction - in the data_sources one. Note that the second level key (here: source) has to exactly match the attributes in the file_path column of the modified sample_annotation.csv (presented below).

library(pepr)
projectConfig = system.file(
"extdata",
paste0("example_peps-", branch),
"example_derived",
"project_config.yaml",
package = "pepr"
)
pepr::.printNestedList(yaml::read_yaml(projectConfig))

Let's introduce a few modifications to the original sample_annotation.csv file to map the appropriate data sources from the project_config.yaml with attributes in the derived column - [file_path]:

library(knitr)
sampleAnnotation = system.file(
"extdata",
paste0("example_peps-", branch),
"example_derived",
"sample_table.csv",
package = "pepr"
)
sampleAnnotationDF = read.table(sampleAnnotation, sep = ",", header = T)
kable(sampleAnnotationDF, format = "html") 

Code

Load pepr and read in the project metadata by specifying the path to the project_config.yaml:

library(pepr)
projectConfig = system.file(
"extdata",
paste0("example_peps-", branch),
"example_derived",
"project_config.yaml",
package = "pepr"
)
p = Project(projectConfig)

And inspect it:

samples(p)

As you can see, the resulting samples are annotated the same way as if they were read from the original, unwieldy, annotations file.

What is more, the p object consists of all the information from the project config file (project_config.yaml). Run the following line to explore it:

config(p)


pepkit/pepr documentation built on Jan. 11, 2020, 11:06 a.m.