flod

library(flod)
#> NB! `flod` is under heavy development and subject to sweeping changes
library(flowCore)

Getting data into your working environment

Read in the .fcs files using flowCore::read.flowSet(). The flowSet is an S4 class and a convenient way of storing related .fcs files in a single object. However, being an S4 object, it is naturally restricted in its scope to the registered methods and, thus, foregoes potentially relevant functions for EDA, transformation, and modelling from other packages.

data(GvHD, package = "flowCore")
GvHD
#> A flowSet with 35 experiments.
#> 
#> An object of class 'AnnotatedDataFrame'
#>   rowNames: s5a01 s5a02 ... s10a07 (35 total)
#>   varLabels: Patient Visit ... name (5 total)
#>   varMetadata: labelDescription
#> 
#> column names(8): FSC-H SSC-H ... FL4-H Time

Turn it into a tibble using flod::to_tibble()

flod::to_tibble(GvHD)
#> # A tibble: 35 × 4
#>    sample_names exprs              keywords           meta_data$Patient $Visit
#>    <chr>        <list>             <list>             <fct>             <fct> 
#>  1 s5a01        <dbl [3,420 × 8]>  <named list [170]> 5                 1     
#>  2 s5a02        <dbl [3,405 × 8]>  <named list [170]> 5                 2     
#>  3 s5a03        <dbl [3,435 × 8]>  <named list [170]> 5                 3     
#>  4 s5a04        <dbl [8,550 × 8]>  <named list [170]> 5                 4     
#>  5 s5a05        <dbl [10,410 × 8]> <named list [170]> 5                 5     
#>  6 s5a06        <dbl [3,750 × 8]>  <named list [170]> 5                 6     
#>  7 s5a07        <dbl [13,979 × 8]> <named list [170]> 5                 7     
#>  8 s6a01        <dbl [2,205 × 8]>  <named list [167]> 6                 1     
#>  9 s6a02        <dbl [13,350 × 8]> <named list [167]> 6                 2     
#> 10 s6a03        <dbl [11,610 × 8]> <named list [167]> 6                 3     
#> # ℹ 25 more rows
#> # ℹ 3 more variables: meta_data$Days <int>, $Grade <int>, $name <chr>

The function defaults to all slots of the flowSet, or accepts a user specified selection:

to_tibble(GvHD, c("exprs", "keywords"))
#> # A tibble: 35 × 2
#>    exprs              keywords          
#>    <list>             <list>            
#>  1 <dbl [3,420 × 8]>  <named list [170]>
#>  2 <dbl [3,405 × 8]>  <named list [170]>
#>  3 <dbl [3,435 × 8]>  <named list [170]>
#>  4 <dbl [8,550 × 8]>  <named list [170]>
#>  5 <dbl [10,410 × 8]> <named list [170]>
#>  6 <dbl [3,750 × 8]>  <named list [170]>
#>  7 <dbl [13,979 × 8]> <named list [170]>
#>  8 <dbl [2,205 × 8]>  <named list [167]>
#>  9 <dbl [13,350 × 8]> <named list [167]>
#> 10 <dbl [11,610 × 8]> <named list [167]>
#> # ℹ 25 more rows

See ?to_tibble for a list of accepted keywords.