Recalculate relative quantities for a given experiment

Recalculate relative quantities for a given experiment

Usage

pcr_rq(x, relative_sample, control_probe = NULL, ...)

# S3 method for class 'pcr'
pcr_rq(x, relative_sample, control_probe = NULL, ...)

# S3 method for class 'data.frame'
pcr_rq(x, relative_sample, control_probe = NULL, ...)

Arguments

x

A pcr or data.frame

relative_sample

A sample to set others relative to (eg my_dmso_sample)

control_probe

Character. target_name to serve as endogenous control.

...

Arguments passed to respective method

Value

An object of same class as x

Examples

dat_path <- system.file("extdata", "untidy-pcr-example.xls", package = "amplify")

read_pcr(dat_path) |>
  pcr_rq("U6D1")
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   .default = col_double(),
#>   `Well Position` = col_character(),
#>   Omit = col_logical(),
#>   `Sample Name` = col_character(),
#>   `Target Name` = col_character(),
#>   Task = col_character(),
#>   Reporter = col_character(),
#>   Quencher = col_character(),
#>   Quantity = col_logical(),
#>   `Quantity Mean` = col_logical(),
#>   `Quantity SD` = col_logical(),
#>   CT = col_character(),
#>   `Delta Ct` = col_logical(),
#>   `Automatic Ct Threshold` = col_logical(),
#>   `Automatic Baseline` = col_logical(),
#>   Comments = col_logical()
#> )
#> ℹ Use `spec()` for the full column specifications.
#> pcr is not tidy, tidying.
#> <pcr[8]>
#> 
#>                              24
#>     ________________________________________________
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 16 | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 
#> 
#> Start corner: tl
#> Plate dimensions: 16 x 24
#> # Experiment type: comparative_ct 
#> # Wells: 384 
#> # Is tidy: TRUE 
#> # Date: 2020-08-21 

# Can also be run after using pcr_control:
read_pcr(dat_path) |>
  pcr_control("GAPDH") |>
  pcr_rq("U6D1")
#> 
#> ── Column specification ────────────────────────────────────────────────────────
#> cols(
#>   .default = col_double(),
#>   `Well Position` = col_character(),
#>   Omit = col_logical(),
#>   `Sample Name` = col_character(),
#>   `Target Name` = col_character(),
#>   Task = col_character(),
#>   Reporter = col_character(),
#>   Quencher = col_character(),
#>   Quantity = col_logical(),
#>   `Quantity Mean` = col_logical(),
#>   `Quantity SD` = col_logical(),
#>   CT = col_character(),
#>   `Delta Ct` = col_logical(),
#>   `Automatic Ct Threshold` = col_logical(),
#>   `Automatic Baseline` = col_logical(),
#>   Comments = col_logical()
#> )
#> ℹ Use `spec()` for the full column specifications.
#> pcr is not tidy, tidying.
#> <pcr[8]>
#> 
#>                              24
#>     ________________________________________________
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 16 | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#>    | ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯ ◯
#> 
#> 
#> Start corner: tl
#> Plate dimensions: 16 x 24
#> # Experiment type: comparative_ct 
#> # Wells: 384 
#> # Is tidy: TRUE 
#> # Date: 2020-08-21