rnanorm.FPKM¶
- class rnanorm.FPKM(gtf=None, gene_lengths=None)[source]¶
Fragments per kilo-base million (FKPM) normalization.
Examples
>>> from rnanorm.datasets import load_toy_data >>> from rnanorm import FPKM >>> dataset = load_toy_data() >>> dataset.exp Gene_1 Gene_2 Gene_3 Gene_4 Gene_5 Sample_1 200 300 500 2000 7000 Sample_2 400 600 1000 4000 14000 Sample_3 200 300 500 2000 17000 Sample_4 200 300 500 2000 2000 >>> fpkm = FPKM(gtf=dataset.gtf_path).set_output(transform="pandas") >>> fpkm.fit_transform(dataset.exp) Gene_1 Gene_2 Gene_3 Gene_4 Gene_5 Sample_1 100000.0 100000.0 100000.0 200000.0 700000.0 Sample_2 100000.0 100000.0 100000.0 200000.0 700000.0 Sample_3 50000.0 50000.0 50000.0 100000.0 850000.0 Sample_4 200000.0 200000.0 200000.0 400000.0 400000.0
- __init__(gtf=None, gene_lengths=None)¶
Initialize class.
Methods
__init__
([gtf, gene_lengths])Initialize class.
fit
(X[, y])Fit transformer by checking X.
fit_transform
(X[, y])Fit to data, then transform it.
get_feature_names_out
([input_features])Get output feature names for transformation.
get_metadata_routing
()Get metadata routing of this object.
get_params
([deep])Get parameters for this estimator.
inverse_transform
(X)Transform X using the inverse function.
set_output
(*[, transform])Set output container.
set_params
(**params)Set the parameters of this estimator.
transform
(X)Transform X using the forward function.