This vignette will show you how and why to use the append functionality of the
The example below demonstrates how to use the constant attributes to define the samples attributes in the
read_type column of the
sample_table.csv file. This functionality is extremely useful when there are many samples that are characterized by identical values of certain attribute (here: value
read_type attribute). Please consider the example below for reference:
As the name suggests the attributes in the specified attributes (here:
read_type) can be defined as constant 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
sample_modifiers.append key-value pair. Note that definition of more than one constant attribute is possible.
Registered S3 method overwritten by 'pryr': method from print.bytes Rcpp pep_version: 2.0.0 sample_table: sample_table.csv sample_modifiers: append: read_type: SINGLE
Let’s introduce a few modifications to the original
sample_table.csv file to use the
sample_modifiers.append section of the config. Simply skip the attributes that are set constant and let the
pepr do the work for you.
pepr and read in the project metadata by specifying the path to the
library(pepr) projectConfig = system.file( "extdata", paste0("example_peps-", branch), "example_append", "project_config.yaml", package = "pepr" ) p = Project(projectConfig) #> Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpSzdJbG/Rinst4b945a77f0f4/pepr/extdata/example_peps-master/example_append/project_config.yaml
And inspect it:
As you can see, the resulting samples are annotated the same way as if they were read from the original annotations file with attributes in the last column manually determined.
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) #> Config object. Class: Config #> pep_version: 2.0.0 #> sample_table: #> /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpSzdJbG/Rinst4b945a77f0f4/pepr/extdata/example_peps-master/example_append/sample_table.csv #> sample_modifiers: #> append: #> read_type: SINGLE #> name: example_append