tests/testthat/_snaps/read-deprecated.md

In bailey-lab/miplicorn: A Framework for Molecular Inversion Probe and Amplicon Analysis

read() is deprecated

`read()` was deprecated in miplicorn 0.2.0.
i Please use `read_tbl_ref_alt_cov()` instead.

read_file() is deprecated

Code
  read_file("small.csv", .name = "ref_umi_count")
Condition
  Warning:
  `read_file()` was deprecated in miplicorn 0.2.0.
  i The function has been replaced by three more specific functions: `read_tbl_reference()`, `read_tbl_alternate()`, and `read_tbl_coverage()`.
Message
  Input detected as the reference table.
Output
  # A reference table: 4 x 8
    sample gene_id gene  mutation   func     aa_chng target ref_umi_count
    <chr>  <chr>   <chr> <chr>      <chr>    <chr>   <chr>          <dbl>
  1 S1     Site1   atp6  atp6-A623E missense A623E   Yes                0
  2 S2     Site1   atp6  atp6-A623E missense A623E   Yes                0
  3 S1     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes               13
  4 S2     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes                0

deprecated read_file() detects reference tables

Code
  read_file("small.csv", .name = "ref_umi_count")
Condition
  Warning:
  `read_file()` was deprecated in miplicorn 0.2.0.
  i The function has been replaced by three more specific functions: `read_tbl_reference()`, `read_tbl_alternate()`, and `read_tbl_coverage()`.
Message
  Input detected as the reference table.
Output
  # A reference table: 4 x 8
    sample gene_id gene  mutation   func     aa_chng target ref_umi_count
    <chr>  <chr>   <chr> <chr>      <chr>    <chr>   <chr>          <dbl>
  1 S1     Site1   atp6  atp6-A623E missense A623E   Yes                0
  2 S2     Site1   atp6  atp6-A623E missense A623E   Yes                0
  3 S1     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes               13
  4 S2     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes                0

deprecated read_file() detects alternate tables

Code
  read_file("small.csv", .name = "alt_umi_count")
Condition
  Warning:
  `read_file()` was deprecated in miplicorn 0.2.0.
  i The function has been replaced by three more specific functions: `read_tbl_reference()`, `read_tbl_alternate()`, and `read_tbl_coverage()`.
Message
  Input detected as the alternate table.
Output
  # An alternate table: 4 x 8
    sample gene_id gene  mutation   func     aa_chng target alt_umi_count
    <chr>  <chr>   <chr> <chr>      <chr>    <chr>   <chr>          <dbl>
  1 S1     Site1   atp6  atp6-A623E missense A623E   Yes                0
  2 S2     Site1   atp6  atp6-A623E missense A623E   Yes                0
  3 S1     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes               13
  4 S2     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes                0

deprecated read_file() detects coverage tables

Code
  read_file("small.csv", .name = "coverage")
Condition
  Warning:
  `read_file()` was deprecated in miplicorn 0.2.0.
  i The function has been replaced by three more specific functions: `read_tbl_reference()`, `read_tbl_alternate()`, and `read_tbl_coverage()`.
Message
  Input detected as the coverage table.
Output
  # A coverage table: 4 x 8
    sample gene_id gene  mutation   func     aa_chng target coverage
    <chr>  <chr>   <chr> <chr>      <chr>    <chr>   <chr>     <dbl>
  1 S1     Site1   atp6  atp6-A623E missense A623E   Yes           0
  2 S2     Site1   atp6  atp6-A623E missense A623E   Yes           0
  3 S1     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes          13
  4 S2     Site2   mdr1  mdr1-N86Y  sense    N86Y    Yes           0

deprecated read_file() fails if can't detect input

Code
  read_file("small.csv")
Condition
  Warning:
  `read_file()` was deprecated in miplicorn 0.2.0.
  i The function has been replaced by three more specific functions: `read_tbl_reference()`, `read_tbl_alternate()`, and `read_tbl_coverage()`.
  Error in `read_file()`:
  ! Unable to detect the type of table input.

bailey-lab/miplicorn documentation built on March 19, 2023, 7:40 p.m.