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Get and set metadata for parameters on a SummarizedExperiment object.

Source: R/se_metadata.R
SE_metadata.Rd

Set metadata for the fitting parameters that define the Metrics assay in SummarizedExperiment object metadata.

Usage

set_SE_fit_parameters(se, value)

set_SE_processing_metadata(se, value)

set_SE_keys(se, value)

set_SE_experiment_metadata(se, value)

set_SE_experiment_raw_data(se, value)

get_SE_fit_parameters(se)

get_SE_processing_metadata(se)

get_SE_experiment_raw_data(se)

get_SE_experiment_metadata(se)

get_SE_keys(se, key_type = NULL)

get_SE_identifiers(se, id_type = NULL, simplify = TRUE)

set_SE_identifiers(se, value)

Arguments

se

a SummarizedExperiment object for which to add fit parameter metadata.

value

named list of metadata for fit parameters.

key_type

string of a specific key type (i.e. 'nested_keys', etc.).

id_type

string of a specific id type (i.e. 'duration', 'cellline_name', etc.).

simplify

Boolean indicating whether output should be simplified.

Value

se with added metadata.

Details

For *et_SE_processing_metadata, get/set metadata for the processing info that defines the date_processed and packages versions in SummarizedExperiment object metadata. For *et_SE_fit_parameters, get/set metadata for fit parameters used to construct the Metrics assay in a SummarizedExperiment object.

Examples

mae <- get_synthetic_data("finalMAE_small.qs") 
se <- mae[[1]]
get_SE_fit_parameters(se)
#> $n_point_cutoff
#> [1] 4
#> 
#> $range_conc
#> [1] 0.005 5.000
#> 
#> $force_fit
#> [1] FALSE
#> 
#> $pcutoff
#> [1] 0.05
#> 
#> $cap
#> [1] 0.1
#> 

mae <- get_synthetic_data("finalMAE_small.qs") 
se <- mae[[1]]
meta <- get_SE_processing_metadata(se)

mae <- get_synthetic_data("finalMAE_small.qs") 
se <- mae[[1]]
get_SE_experiment_raw_data(se)
#> NULL

mae <- get_synthetic_data("finalMAE_small.qs") 
se <- mae[[1]]
get_SE_experiment_metadata(se)
#> DataFrame with 0 rows and 0 columns

mae <- get_synthetic_data("finalMAE_small.qs") 
se <- mae[[1]]
get_SE_identifiers(se)
#> $duration
#> [1] "Duration"
#> 
#> $cellline
#> [1] "clid"
#> 
#> $cellline_name
#> [1] "CellLineName"
#> 
#> $cellline_tissue
#> [1] "Tissue"
#> 
#> $cellline_ref_div_time
#> [1] "ReferenceDivisionTime"
#> 
#> $cellline_parental_identifier
#> [1] "parental_identifier"
#> 
#> $cellline_subtype
#> [1] "subtype"
#> 
#> $drug
#> [1] "Gnumber"
#> 
#> $drug_name
#> [1] "DrugName"
#> 
#> $drug_moa
#> [1] "drug_moa"
#> 
#> $untreated_tag
#> [1] "vehicle"   "untreated"
#> 
#> $masked_tag
#> [1] "masked"
#> 
#> $well_position
#> [1] "WellRow"    "WellColumn"
#> 
#> $concentration
#> [1] "Concentration"
#> 
#> $template
#> [1] "Template"  "Treatment"
#> 
#> $barcode
#> [1] "Barcode" "Plate"  
#> 
#> $drug2
#> [1] "Gnumber_2"
#> 
#> $drug_name2
#> [1] "DrugName_2"
#> 
#> $drug_moa2
#> [1] "drug_moa_2"
#> 
#> $concentration2
#> [1] "Concentration_2"
#> 
#> $drug3
#> [1] "Gnumber_3"
#> 
#> $drug_name3
#> [1] "DrugName_3"
#> 
#> $drug_moa3
#> [1] "drug_moa_3"
#> 
#> $concentration3
#> [1] "Concentration_3"
#> 
#> $data_source
#> [1] "data_source"
#> 
#> $replicate
#> [1] "Replicate"
#>