Get available plates or apply function to them

Description

Get all plates contained in an OPMS object or a list, or create a list containing a single OPM object as element, or apply a function to a collection of OPM objects.

Usage

  ## S4 method for signature 'MOPMX'
oapply(object, fun, ..., simplify = TRUE)
  ## S4 method for signature 'OPM'
oapply(object, fun, ..., simplify = TRUE)
  ## S4 method for signature 'OPMS'
oapply(object, fun, ..., simplify = TRUE)

  ## S4 method for signature 'MOPMX'
plates(object) 
  ## S4 method for signature 'WMD'
plates(object) 
  ## S4 method for signature 'WMDS'
plates(object) 
  ## S4 method for signature 'list'
plates(object) 

Arguments

Details

The list method of plates traverses the input recursively and skips all objects of other classes than OPM. See also opms, which is somewhat similar but more flexible.

oapply applies a function to all OPM objects within an OPMS object. Optionally it simplifies the result to an OPMS object if possible, or other structures simpler than a list. The OPM method of oapply simply applies fun once (to object).

Value

For plates, a list of OPM objects (may be empty instead if object is a list). The result of oapply depends on fun and simplify: a list, vector, matrix or OPMS object are possible outcomes.

See Also

base::list base::as.list base::sapply

Other conversion-functions: as.data.frame, extract, extract_columns, flatten, merge, opmx, rep, rev, sort, split, to_yaml, unique

Examples

# plates(), 'OPM' method
summary(x <- plates(vaas_1)) # => list of OPM objects

##      Length Class Mode
## [1,] 1      OPMD  S4

stopifnot(is.list(x), length(x) == 1L, sapply(x, inherits, what = "OPM"))

# plates(), 'OPMS' method
summary(x <- plates(vaas_4)) # => list of OPM objects

##      Length Class Mode
## [1,] 1      OPMD  S4  
## [2,] 1      OPMD  S4  
## [3,] 1      OPMD  S4  
## [4,] 1      OPMD  S4

stopifnot(is.list(x), length(x) == 4L, sapply(x, inherits, what = "OPM"))

# plates(), list method
x <- list(vaas_1, letters, vaas_4, 1:10)
summary(x <- plates(x)) # => list of OPM objects

##      Length Class Mode
## [1,] 1      OPMD  S4  
## [2,] 1      OPMD  S4  
## [3,] 1      OPMD  S4  
## [4,] 1      OPMD  S4  
## [5,] 1      OPMD  S4

stopifnot(is.list(x), length(x) == 5, sapply(x, inherits, what = "OPM"))

## oapply()
summary(x <- oapply(vaas_4, identity)) # trivial

## 1
## Class                 OPMD
## From file             ./E. coli DSM
##                       18039_vim10_12B__1_28_PMX_0_8#30#2010_E_12B_5.csv
## Hours measured        95.75
## Number of wells       96
## Plate type            Gen III
## Position              12-B
## Setup time            8/30/2010 1:19:11 PM
## Metadata              5
## Aggregated            TRUE
## Discretized           TRUE
## 
## 2
## Class                 OPMD
## From file             ./E. coli DSM
##                       30083T_vim10_7B__1_28_PMX_0_8#30#2010_F_
##                       7B_5.csv
## Hours measured        95.75
## Number of wells       96
## Plate type            Gen III
## Position              7-B
## Setup time            8/30/2010 1:53:08 PM
## Metadata              5
## Aggregated            TRUE
## Discretized           TRUE
## 
## 3
## Class                 OPMD
## From file             ./P. aeruginosa DSM
##                       1707_vim10_17B__1_28_PMX_0_8#30#2010_D_17B_5.csv
## Hours measured        95.75
## Number of wells       96
## Plate type            Gen III
## Position              17-B
## Setup time            8/30/2010 12:31:46 PM
## Metadata              5
## Aggregated            TRUE
## Discretized           TRUE
## 
## 4
## Class                 OPMD
## From file             ./P. aeruginosa St.
##                       429_vim10_22B__1_28_PMX_0_8#30#2010_C_22B_5.csv
## Hours measured        95.75
## Number of wells       96
## Plate type            Gen III
## Position              22-B
## Setup time            8/30/2010 11:28:54 AM
## Metadata              5
## Aggregated            TRUE
## Discretized           TRUE
## 
## => OPMS object with 4 plates (4 aggregated, 4 discretized) of type 'Gen III', 96 well(s) and about 384 time point(s).

stopifnot(identical(x, vaas_4))
summary(x <- oapply(vaas_4, identity, simplify = FALSE)) # => yields list

##      Length Class Mode
## [1,] 1      OPMD  S4  
## [2,] 1      OPMD  S4  
## [3,] 1      OPMD  S4  
## [4,] 1      OPMD  S4

stopifnot(is.list(x), length(x) == 4, sapply(x, class) == "OPMD")