tests/testthat/_snaps/data_handling.md

In simondrue/castle: Fortify your ddPCR analyses for low-frequency variant detection

single import

Code
  single_import_patient %>% data.frame()
Output
         FileName           Sample Well Ch1TargetType Ch2TargetType        Target
  1 patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown KRAS G12D mut
  2 patient_1.csv Patient1 PlasmaA  A01       Unknown       Unknown KRAS G12D mut
  3 patient_1.csv Patient1 PlasmaA  B01       Unknown       Unknown KRAS G12D mut
  4 patient_1.csv          Control  C01       Unknown       Unknown KRAS G12D mut
    DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1                  70449                17647                 20
  2                  11147                 2771                  1
  3                  11871                 3002                  2
  4                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      2         88118                   2   (A01,B01)
  2                      0         13919                   1        <NA>
  3                      0         14875                   1        <NA>
  4                      0         14875                   1        <NA>

Code
  merge_wells_yes_import_patient %>% data.frame()
Output
         FileName           Sample Well Ch1TargetType Ch2TargetType        Target
  1 patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown KRAS G12D mut
  2 patient_1.csv          Control  C01       Unknown       Unknown KRAS G12D mut
    DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1                  23018                 5773                  3
  2                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      0         28794                   2   (A01,B01)
  2                      0         14875                   1        <NA>

Code
  merge_wells_no_import_patient %>% data.frame()
Output
         FileName           Sample Well Ch1TargetType Ch2TargetType        Target
  1 patient_1.csv Patient1 PlasmaA  A01       Unknown       Unknown KRAS G12D mut
  2 patient_1.csv Patient1 PlasmaA  B01       Unknown       Unknown KRAS G12D mut
  3 patient_1.csv          Control  C01       Unknown       Unknown KRAS G12D mut
    DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1                  11147                 2771                  1
  2                  11871                 3002                  2
  3                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      0         13919                   1        <NA>
  2                      0         14875                   1        <NA>
  3                      0         14875                   1        <NA>

Code
  merge_wells_QS_import_patient %>% data.frame()
Output
         FileName           Sample Well Ch1TargetType Ch2TargetType        Target
  1 patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown KRAS G12D mut
  2 patient_1.csv          Control  C01       Unknown       Unknown KRAS G12D mut
    DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1                  70449                17647                 20
  2                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      2         88118                   2   (A01,B01)
  2                      0         14875                   1        <NA>

multi import

Code
  multi_import_patient %>% data.frame()
Output
                FileName           Sample Well Ch1TargetType Ch2TargetType
  1        patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown
  2        patient_1.csv Patient1 PlasmaA  A01       Unknown       Unknown
  3        patient_1.csv Patient1 PlasmaA  B01       Unknown       Unknown
  4        patient_1.csv          Control  C01       Unknown       Unknown
  5        patient_2.csv Patient2 PlasmaA  M01       Unknown       Unknown
  6        patient_2.csv Patient2 PlasmaA  A01       Unknown       Unknown
  7        patient_2.csv Patient2 PlasmaA  B01       Unknown       Unknown
  8  patient_2_extra.csv Patient2 PlasmaA  M01       Unknown       Unknown
  9  patient_2_extra.csv Patient2 PlasmaA  A01       Unknown       Unknown
  10 patient_2_extra.csv Patient2 PlasmaA  B01       Unknown       Unknown
            Target DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1  KRAS G12D mut                  70449                17647                 20
  2  KRAS G12D mut                  11147                 2771                  1
  3  KRAS G12D mut                  11871                 3002                  2
  4  KRAS G12D mut                  11871                 3002                  2
  5  KRAS G12D mut                  70449                17647                 20
  6  KRAS G12D mut                  11147                 2771                  1
  7  KRAS G12D mut                  11871                 3002                  2
  8  KRAS G12D mut                  70449                17647                 20
  9  KRAS G12D mut                  11147                 2771                  1
  10 KRAS G12D mut                  11871                 3002                  2
     DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                       2         88118                   2   (A01,B01)
  2                       0         13919                   1        <NA>
  3                       0         14875                   1        <NA>
  4                       0         14875                   1        <NA>
  5                       2         88118                   2   (A01,B01)
  6                       0         13919                   1        <NA>
  7                       0         14875                   1        <NA>
  8                       2         88118                   2   (A01,B01)
  9                       0         13919                   1        <NA>
  10                      0         14875                   1        <NA>

Code
  merge_wells_yes_import_patient %>% data.frame()
Output
               FileName           Sample Well Ch1TargetType Ch2TargetType
  1       patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown
  2       patient_2.csv Patient2 PlasmaA  M02       Unknown       Unknown
  3 patient_2_extra.csv Patient2 PlasmaA  M03       Unknown       Unknown
  4       patient_1.csv          Control  C01       Unknown       Unknown
           Target DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1 KRAS G12D mut                  23018                 5773                  3
  2 KRAS G12D mut                  23018                 5773                  3
  3 KRAS G12D mut                  23018                 5773                  3
  4 KRAS G12D mut                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      0         28794                   2   (A01,B01)
  2                      0         28794                   2   (A01,B01)
  3                      0         28794                   2   (A01,B01)
  4                      0         14875                   1        <NA>

Code
  merge_wells_no_import_patient %>% data.frame()
Output
               FileName           Sample Well Ch1TargetType Ch2TargetType
  1       patient_1.csv Patient1 PlasmaA  A01       Unknown       Unknown
  2       patient_1.csv Patient1 PlasmaA  B01       Unknown       Unknown
  3       patient_1.csv          Control  C01       Unknown       Unknown
  4       patient_2.csv Patient2 PlasmaA  A01       Unknown       Unknown
  5       patient_2.csv Patient2 PlasmaA  B01       Unknown       Unknown
  6 patient_2_extra.csv Patient2 PlasmaA  A01       Unknown       Unknown
  7 patient_2_extra.csv Patient2 PlasmaA  B01       Unknown       Unknown
           Target DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1 KRAS G12D mut                  11147                 2771                  1
  2 KRAS G12D mut                  11871                 3002                  2
  3 KRAS G12D mut                  11871                 3002                  2
  4 KRAS G12D mut                  11147                 2771                  1
  5 KRAS G12D mut                  11871                 3002                  2
  6 KRAS G12D mut                  11147                 2771                  1
  7 KRAS G12D mut                  11871                 3002                  2
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      0         13919                   1        <NA>
  2                      0         14875                   1        <NA>
  3                      0         14875                   1        <NA>
  4                      0         13919                   1        <NA>
  5                      0         14875                   1        <NA>
  6                      0         13919                   1        <NA>
  7                      0         14875                   1        <NA>

Code
  merge_wells_and_files_import_patient %>% data.frame()
Output
                             FileName           Sample Well Ch1TargetType
  1                     patient_1.csv Patient1 PlasmaA  M01       Unknown
  2 patient_2.csv,patient_2_extra.csv Patient2 PlasmaA  M02       Unknown
  3                     patient_1.csv          Control  C01       Unknown
    Ch2TargetType        Target DoubleNegativeDroplets WildtypeOnlyDroplets
  1       Unknown KRAS G12D mut                  23018                 5773
  2       Unknown KRAS G12D mut                  46036                11546
  3       Unknown KRAS G12D mut                  11871                 3002
    MutantOnlyDroplets DoublePositiveDroplets TotalDroplets NumberOfMergedWells
  1                  3                      0         28794                   2
  2                  6                      0         57588                   4
  3                  2                      0         14875                   1
          MergedWells
  1         (A01,B01)
  2 (A01,B01,A01,B01)
  3              <NA>

Code
  merge_wells_QS_import_patient %>% data.frame()
Output
               FileName           Sample Well Ch1TargetType Ch2TargetType
  1       patient_1.csv Patient1 PlasmaA  M01       Unknown       Unknown
  2       patient_1.csv          Control  C01       Unknown       Unknown
  3       patient_2.csv Patient2 PlasmaA  M01       Unknown       Unknown
  4 patient_2_extra.csv Patient2 PlasmaA  M01       Unknown       Unknown
           Target DoubleNegativeDroplets WildtypeOnlyDroplets MutantOnlyDroplets
  1 KRAS G12D mut                  70449                17647                 20
  2 KRAS G12D mut                  11871                 3002                  2
  3 KRAS G12D mut                  70449                17647                 20
  4 KRAS G12D mut                  70449                17647                 20
    DoublePositiveDroplets TotalDroplets NumberOfMergedWells MergedWells
  1                      2         88118                   2   (A01,B01)
  2                      0         14875                   1        <NA>
  3                      2         88118                   2   (A01,B01)
  4                      2         88118                   2   (A01,B01)

simondrue/castle documentation built on Jan. 29, 2022, 3:04 a.m.