tests/testthat/_snaps/sample_metadata.md

In cancerit/RCRISPR: R Functions for CRISPR-Related Analyses

read sample metadata

Code
  test_sample_metadata
Output
  An object of class "SampleMetadata"
  Slot "filepath":
  [1] "test"

  Slot "filename_column":
  [1] 5

  Slot "label_column":
  [1] 1

  Slot "plasmid_column":
  [1] 2

  Slot "control_column":
  [1] 3

  Slot "treatment_column":
  [1] 4

  Slot "group_column":
  [1] 6

  Slot "reads_column":
  [1] 7

  Slot "file_separator":
  [1] "\t"

  Slot "file_header":
  [1] TRUE

  Slot "metadata":
              filename          label plasmid control treatment     group
  1    test_counts.tsv        HELA_T0       1       0         0        T0
  2 test_counts.tsv.gz CTRL_HELA_T15A       0       1         0 T15A_CTRL
       reads  X
  1 30000000 NA
  2 30000000 NA

get processed sample metadata with reads and group

Code
  get_sample_metadata(test_sample_metadata, processed = T)
Output
    filename              label plasmid control treatment     group    reads
  1        0    test_counts.tsv    <NA>       1         0        T0 30000000
  2        0 test_counts.tsv.gz    <NA>       0         1 T15A_CTRL 30000000

get processed sample metadata with reads only

Code
  get_sample_metadata(test_sample_metadata, processed = T)
Output
    filename              label plasmid control treatment    reads
  1        0    test_counts.tsv    <NA>       1         0 30000000
  2        0 test_counts.tsv.gz    <NA>       0         1 30000000

get processed sample metadata with group only

Code
  get_sample_metadata(test_sample_metadata, processed = T)
Output
    filename              label plasmid control treatment     group
  1        0    test_counts.tsv    <NA>       1         0        T0
  2        0 test_counts.tsv.gz    <NA>       0         1 T15A_CTRL

get unprocessed sample metadata with reads and group

Code
  get_sample_metadata(test_sample_metadata, processed = F)
Output
              filename          label plasmid control treatment     group
  1    test_counts.tsv        HELA_T0       1       0         0        T0
  2 test_counts.tsv.gz CTRL_HELA_T15A       0       1         0 T15A_CTRL
       reads  X
  1 30000000 NA
  2 30000000 NA

get unprocessed sample metadata with reads only

Code
  get_sample_metadata(test_sample_metadata, processed = F)
Output
              filename          label plasmid control treatment     group
  1    test_counts.tsv        HELA_T0       1       0         0        T0
  2 test_counts.tsv.gz CTRL_HELA_T15A       0       1         0 T15A_CTRL
       reads  X
  1 30000000 NA
  2 30000000 NA

get unprocessed sample metadata with group only

Code
  get_sample_metadata(test_sample_metadata, processed = F)
Output
              filename          label plasmid control treatment     group
  1    test_counts.tsv        HELA_T0       1       0         0        T0
  2 test_counts.tsv.gz CTRL_HELA_T15A       0       1         0 T15A_CTRL
       reads  X
  1 30000000 NA
  2 30000000 NA

cancerit/RCRISPR documentation built on April 26, 2023, 10:12 p.m.