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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, append = TRUE)

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.

append

Boolean indicating whether to append the new metadata value to the existing entry.

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"
#>