Summary Method for AnyHermesData Objects

Provides a concise summary of the content of AnyHermesData objects.

Usage

summary(object, ...)

# S4 method for class 'AnyHermesData'
summary(object)

# S4 method for class 'HermesDataSummary'
show(object)

Arguments

object: (HermesDataSummary)
result from the summary method applied to AnyHermesData object.
...: not used.

Value

An object of the corresponding summary class, here HermesDataSummary.

Methods (by class)

summary(AnyHermesData): A summary method for AnyHermesData object that creates a HermesDataSummary object.
show(HermesDataSummary): A show method prints summary description of HermesDataSummary object generated by the summary() method.

Examples

object <- hermes_data
object_summary <- summary(object)

# We can access parts of this S4 object with the `slot` function.
str(object_summary)
#> Formal class 'HermesDataSummary' [package "hermes"] with 10 slots
#>   ..@ class_name            : chr "HermesData"
#>   ..@ n_genes               : int 5085
#>   ..@ n_samples             : int 20
#>   ..@ additional_gene_info  : chr [1:3] "GeneID" "SYMBOL" "chromosome_name"
#>   ..@ additional_sample_info: chr [1:72] "Filename" "SampleID" "AGEGRP" "AGE18" ...
#>   ..@ no_qc_flags_filled    : logi FALSE
#>   ..@ genes_fail            : chr [1:3021] "GeneID:10677" "GeneID:101928428" "GeneID:100422835" "GeneID:102466731" ...
#>   ..@ samples_fail          : chr [1:2] "06520063C0043R" "06520062C0017R"
#>   ..@ lib_sizes             : Named num [1:20] 5474927 5154958 4632496 5533212 5026848 ...
#>   .. ..- attr(*, "names")= chr [1:20] "06520011B0023R" "06520067C0018R" "06520063C0043R" "06520105C0017R" ...
#>   ..@ assay_names           : chr "counts"
slotNames(object_summary)
#>  [1] "class_name"             "n_genes"                "n_samples"             
#>  [4] "additional_gene_info"   "additional_sample_info" "no_qc_flags_filled"    
#>  [7] "genes_fail"             "samples_fail"           "lib_sizes"             
#> [10] "assay_names"           
slot(object_summary, "lib_sizes")
#> 06520011B0023R 06520067C0018R 06520063C0043R 06520105C0017R 06520092C0017R 
#>        5474927        5154958        4632496        5533212        5026848 
#> 06520103C0017R 06520001B0023R 06520022C0017R 06520062C0017R 06520046C0018R 
#>        7262374        6408552        5286953        4778014        4990556 
#> 06520101B0017R 06520047C0017R 06520024B0014R 06520080B0023R 06520093C0017R 
#>        4923925        5417510        5560720        4642530        5016838 
#> 06520070C0018R 06520023C0018R 06520099B0017R 06520015C0016R 06520019C0023R 
#>        6464043        6080233        5314431        5426566        6139497 

# Just calling the summary method like this will use the `show()` method.
summary(object)
#> HermesData object with 20 samples of 5085 genes.
#> - Library sizes across samples: mean 5476759, median 5365970, range 4632496 to 7262374
#> - Included assays (1): counts
#> - Additional gene information (3): GeneID SYMBOL chromosome_name
#> - Additional sample information (72): Filename SampleID ... TTYPE
#>   STDSSDY
#> - Low expression genes (3021): GeneID:10677 GeneID:101928428 ...
#>   GeneID:9084 GeneID:9426
#> - Samples with too low depth or technical failures (2): 06520063C0043R
#>   06520062C0017R