Example 1: basic sample subannotation table

This example demonstrates how the sample subannotation functionality is used. In this example, 2 samples have multiple input files that need merging (frog_1 and frog_2), while 1 sample (frog_3) does not. Therefore, frog_3 specifies its file in the sample_table.csv file, while the others leave that field blank and instead specify several files in the subsample_table.csv file.

This example is made up of these components:

• Project config file:

   pep_version: 2.0.0
   sample_table: sample_table.csv
   subsample_table: subsample_table.csv
   output_dir: $HOME/example_results

• Sample table:

  sample_name	protocol	file
  frog_1	anySampleType	multi
  frog_2	anySampleType	multi
  frog_3	anySampleType	multi

• Subsample table:

  sample_name	subsample_name	file
  frog_1	sub_a	data/frog1a_data.txt
  frog_1	sub_b	data/frog1b_data.txt
  frog_1	sub_c	data/frog1c_data.txt
  frog_2	sub_a	data/frog2a_data.txt
  frog_2	sub_b	data/frog2b_data.txt

Let’s create the Project object and see if multiple files are present

projectConfig1 = system.file(
"extdata",
paste0("example_peps-", branch),
"example_subtable1",
"project_config.yaml",
package = "pepr"
)
p1 = Project(projectConfig1)
#> Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/example_peps-master/example_subtable1/project_config.yaml
# Check the files
p1Samples = sampleTable(p1)
p1Samples$file
#> [[1]]
#> [1] "data/frog1a_data.txt" "data/frog1b_data.txt" "data/frog1c_data.txt"
#> 
#> [[2]]
#> [1] "data/frog2a_data.txt" "data/frog2b_data.txt"
#> 
#> [[3]]
#> [1] "multi"
# Check the subsample names
p1Samples$subsample_name
#> [[1]]
#> [1] "sub_a" "sub_b" "sub_c"
#> 
#> [[2]]
#> [1] "sub_a" "sub_b"
#> 
#> [[3]]
#> NULL

And inspect the whole table in p1@samples slot

You can also access a single subsample if you call the getSubsample method with appropriate sample_name - subsample_name attribute combination. Note, that this is only possible if the subsample_name column is defined in the sub_annotation.csv file.

sampleName = "frog_1"
subsampleName = "sub_a"
getSubsample(p1, sampleName, subsampleName)
#>    sample_name      protocol                 file subsample_name
#> 1:      frog_1 anySampleType data/frog1a_data.txt          sub_a

Example 2: subannotations and derived attributes

This example uses a subsample_table.csv file and a derived attributes to point to files. This is a rather complex example. Notice we must include the file_id column in the sample_table.csv file, and leave it blank; this is then populated by just some of the samples (frog_1 and frog_2) in the subsample_table.csv, but is left empty for the samples that are not merged.

This example is made up of these components:

• Project config file:

  Warning in readLines(file): incomplete final line found on '/private/var/
  folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/
  extdata/example_peps-master/example_subtable2/project_config.yaml'
   pep_version: 2.0.0
   sample_table: sample_table.csv
   subsample_table: subsample_table.csv
   output_dir: $HOME/hello_looper_results
   pipeline_interfaces: ../pipeline/pipeline_interface.yaml
   sample_modifiers:
      derive:
          attributes: file
          sources:
              local_files: ../data/{identifier}{file_id}_data.txt
              local_files_unmerged: ../data/{identifier}_data.txt

• Sample annotation table:

#> Warning in read.table(sampleAnnotation, sep = ",", header = T): incomplete
#> final line found by readTableHeader on '/private/var/folders/3f/
#> 0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/
#> example_peps-master/example_subtable2/sample_table.csv'

• Sample subannotation table:

  sample_name	file_id	subsample_name
  frog_1	a	a
  frog_1	b	b
  frog_1	c	c
  frog_2	a	a
  frog_2	b	b

  Let’s load the project config, create the Project object and see if multiple files are present

projectConfig2 = system.file(
"extdata",
paste0("example_peps-", branch),
"example_subtable2",
"project_config.yaml",
package = "pepr"
)
p2 = Project(projectConfig2)
#> Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/example_peps-master/example_subtable2/project_config.yaml
#> Warning in readLines(con): incomplete final line found on '/private/var/folders/
#> 3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/
#> example_peps-master/example_subtable2/project_config.yaml'
#> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 3 rows to
#> replace 1 rows
#> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 2 rows to
#> replace 1 rows
# Check the files
p2Samples = sampleTable(p2)
p2Samples$file
#> [[1]]
#> [1] "../data/frog1a_data.txt"
#> 
#> [[2]]
#> [1] "../data/frog2a_data.txt"
#> 
#> [[3]]
#> [1] "../data/frog3_data.txt"
#> 
#> [[4]]
#> [1] "../data/frog4_data.txt"

And inspect the whole table in p2@samples slot

Example 3: subannotations and expansion characters

This example gives the exact same results as Example 2, but in this case, uses a wildcard for frog_2 instead of including it in the subsample_table.csv file. Since we can’t use a wildcard and a subannotation for the same sample, this necessitates specifying a second data source class (local_files_unmerged) that uses an asterisk (*). The outcome is the same.

This example is made up of these components:

• Project config file:

   pep_version: 2.0.0
   sample_table: sample_table.csv
   subsample_table: subsample_table.csv
   output_dir: $HOME/hello_looper_results
   pipeline_interfaces: ../pipeline/pipeline_interface.yaml
   sample_modifiers:
      derive:
          attributes: file
          sources:
              local_files: ../data/{identifier}{file_id}_data.txt
              local_files_unmerged: ../data/{identifier}*_data.txt

• Sample annotation table:

  sample_name	protocol	identifier	file	file_id
  frog_1	anySampleType	frog1	local_files	NA
  frog_2	anySampleType	frog2	local_files_unmerged	NA
  frog_3	anySampleType	frog3	local_files_unmerged	NA
  frog_4	anySampleType	frog4	local_files_unmerged	NA

• Sample subtable table:

  sample_name	file_id
  frog_1	a
  frog_1	b
  frog_1	c

  Let’s load the project config, create the Project object and see if multiple files are present

projectConfig3 = system.file(
"extdata",
paste0("example_peps-", branch),
"example_subtable3",
"project_config.yaml",
package = "pepr"
)
p3 = Project(projectConfig3)
#> Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/example_peps-master/example_subtable3/project_config.yaml
#> Warning in `[<-.data.frame`(x, i, j, value): replacement element 1 has 3 rows to
#> replace 1 rows
# Check the files
p3Samples = sampleTable(p3)
p3Samples$file
#> [[1]]
#> [1] "../data/frog1a_data.txt"
#> 
#> [[2]]
#> [1] "../data/frog2*_data.txt"
#> 
#> [[3]]
#> [1] "../data/frog3*_data.txt"
#> 
#> [[4]]
#> [1] "../data/frog4*_data.txt"

And inspect the whole table in p3@samples slot

Example 4: subannotations and multiple (separate-class) inputs

Merging is for same class inputs (like, multiple files for read1). Different-class inputs (like read1 vs read2) are handled by different attributes (or columns). This example shows you how to handle paired-end data, while also merging within each.

This example is made up of these components:

• Project config file:

   pep_version: 2.0.0
   sample_table: sample_table.csv
   subsample_table: subsample_table.csv
   output_dir: $HOME/hello_looper_results
   pipeline_interfaces: ../pipeline/pipeline_interface.yaml

• Sample annotation table:

  sample_name	protocol
  frog_1	anySampleType
  frog_2	anySampleType
  frog_3	anySampleType
  frog_4	anySampleType

• Sample subannotation table:

  sample_name	read1	read2
  frog_1	frog1a_data.txt	frog1a_data2.txt
  frog_1	frog1b_data.txt	frog1b_data2.txt
  frog_1	frog1c_data.txt	frog1b_data2.txt

  Let’s load the project config, create the Project object and see if multiple files are present

projectConfig4 = system.file(
"extdata",
paste0("example_peps-", branch),
"example_subtable4",
"project_config.yaml",
package = "pepr"
)
p4 = Project(projectConfig4)
#> Loading config file: /private/var/folders/3f/0wj7rs2144l9zsgxd3jn5nxc0000gn/T/RtmpF0yVmb/Rinstbd5d643c109c/pepr/extdata/example_peps-master/example_subtable4/project_config.yaml
# Check the read1 and read2 columns
p4Samples = sampleTable(p4)
p4Samples$read1
#> [[1]]
#> [1] "frog1a_data.txt" "frog1b_data.txt" "frog1c_data.txt"
#> 
#> [[2]]
#> NULL
#> 
#> [[3]]
#> NULL
#> 
#> [[4]]
#> NULL
p4Samples$read2
#> [[1]]
#> [1] "frog1a_data2.txt" "frog1b_data2.txt" "frog1b_data2.txt"
#> 
#> [[2]]
#> NULL
#> 
#> [[3]]
#> NULL
#> 
#> [[4]]
#> NULL

And inspect the whole table in p4@samples slot