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Save and Restore IsoformicExperiment Objects as Parquet

Source: R/IsoformicExperiment-io.R
isoformic-io.Rd

write_isoformic() writes an IsoformicExperiment to a directory of Parquet files and read_isoformic() restores it. The layout is:

<path>/
  experiment.parquet        key/value: experiment_name, annot_path, ...
  col_data.parquet          sample metadata
  metadata.parquet          key/value: scalar entries of `metadata`
  tx_type_palette.parquet   transcript_type, color
  assays/<name>.parquet     transcript_id + one column per sample
  gene_assays/<name>.parquet  only explicitly set gene assays
  dea/det.parquet, dea/deg.parquet, dea/cutoffs.parquet
  gsea/<name>.parquet
  annotation/               copy of the annotation directory (optional)

With copy_annotation = TRUE the annotation directory is copied inside the experiment directory so that the result is self-contained and portable. Otherwise annot_path is stored as an absolute path and must still exist when the object is read back (it can be overridden with the annot_path argument of read_isoformic()).

Usage

write_isoformic(
  self,
  path = NULL,
  overwrite = FALSE,
  copy_annotation = FALSE,
  ...
)

read_isoformic(path, annot_path = NULL)

Arguments

self

An IsoformicExperiment.

path

Directory to write to or read from. For write_isoformic() defaults to the object's data_path, or to get_isoformic_cache("experiments", experiment_name).

overwrite

Logical, replace an existing directory.

copy_annotation

Logical, copy the annotation directory inside path.

...

Passed on to methods.

annot_path

Optional annotation directory overriding the stored one when reading.

Value

write_isoformic() returns the object with data_path set, invisibly. read_isoformic() returns an IsoformicExperiment.

Examples

iso <- example_isoformic()
dir <- file.path(tempdir(), "iso_example")
iso <- write_isoformic(iso, dir, overwrite = TRUE, copy_annotation = TRUE)
list.files(dir, recursive = TRUE)
#>  [1] "annotation/annot_data_exons.parquet"      
#>  [2] "annotation/annot_data_genes.parquet"      
#>  [3] "annotation/annot_data_sequences.parquet"  
#>  [4] "annotation/annot_data_transcripts.parquet"
#>  [5] "annotation/annot_metadata.parquet"        
#>  [6] "annotation/annot_seq_regions.parquet"     
#>  [7] "assays/abundance.parquet"                 
#>  [8] "assays/counts.parquet"                    
#>  [9] "col_data.parquet"                         
#> [10] "dea/deg.parquet"                          
#> [11] "dea/det.parquet"                          
#> [12] "experiment.parquet"                       
#> [13] "metadata.parquet"                         
#> [14] "tx_type_palette.parquet"                  
iso2 <- read_isoformic(dir)
identical(assay(iso), assay(iso2))
#> [1] TRUE