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Get the normalization

Source: R/screenr-class.R
get_normalization.Rd

Returns the normalization of a ScreenR object, as set by normalize_data: the method, the effective library size of each sample and how it was obtained. The same normalization is used by all the functions of the analysis: the normalized counts, the data table, the plots and the offsets of the edgeR and limma models.

Usage

get_normalization(object)

Arguments

object

The ScreenR object obtained using create_screenr_object.

Value

NULL when the object is not normalized; otherwise a list with:

  • method: "cpm", "tmm", "control" or "custom" (set with set_normalized_count_table);

  • effective_library_size: the effective library size of each sample of the object (the normalized count of a barcode is its raw count divided by the effective library size, times 1e6);

  • reference: the identifiers of the control barcodes (method "control"), otherwise NULL;

  • and the provenance recorded when the normalization was computed: library_size (the total raw counts of each sample), norm_factors (the TMM factors for "tmm", otherwise 1), n_barcodes (the number of barcodes of the object) and screenr_version.

The provenance describes the object when it was normalized: after subsetting, the effective library sizes of the retained samples are kept unchanged.

See also

normalize_data

Examples

object <- get0("object", envir = asNamespace("ScreenR"))
get_normalization(object)$method
#> [1] "cpm"
get_normalization(normalize_data(object, method = "tmm"))
#> $method
#> [1] "tmm"
#> 
#> $effective_library_size
#>          T1          T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C     Time3_A 
#>    10853404     9827013     6840595     9229604     9737088     9647737 
#>     Time3_B     Time3_C Time4_TRT_A Time4_TRT_B Time4_TRT_C     Time4_A 
#>     9179789     9641856     8799318     9717098    12044656    10302865 
#>     Time4_B     Time4_c 
#>     9128760     9182589 
#> 
#> $reference
#> NULL
#> 
#> $library_size
#>          T1          T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C     Time3_A 
#>    10671757     9799724     6824877     9107354     9717868     9485195 
#>     Time3_B     Time3_C Time4_TRT_A Time4_TRT_B Time4_TRT_C     Time4_A 
#>     9016812     9568624     8933915     9883209    12325124    10351136 
#>     Time4_B     Time4_c 
#>     9180192     9315365 
#> 
#> $norm_factors
#>          T1          T2 Time3_TRT_A Time3_TRT_B Time3_TRT_C     Time3_A 
#>   1.0170212   1.0027846   1.0023031   1.0134232   1.0019778   1.0171364 
#>     Time3_B     Time3_C Time4_TRT_A Time4_TRT_B Time4_TRT_C     Time4_A 
#>   1.0180748   1.0076534   0.9849342   0.9831926   0.9772442   0.9953367 
#>     Time4_B     Time4_c 
#>   0.9943974   0.9857466 
#> 
#> $n_barcodes
#> [1] 5320
#> 
#> $screenr_version
#> [1] "1.15.16"
#>