pyrnaither.stats.qc_todo module
Placeholder implementations for functions that need to be implemented.
- pyrnaither.stats.qc_todo.generate_replicate_matrix(data, min_reps, col, anno)[source]
Generate a replicate matrix from the given data.
- Return type:
Tuple[ndarray,List[int],List[int]]- Parameters:
data (DataFrame)
min_reps (int)
col (str)
anno (str)
- Args:
data: DataFrame containing at least columns [col4val, col4anno]. min_reps: Minimum number of replicates required to keep an ID. col: name of the intensity column to fetch when index_or_int=”Intensities”. anno: name of the annotation column grouping replicates.
- Returns:
- replicate_matrix: 2D numpy array of shape (n_items, max_replicates), filled with
indices or values, using np.nan where missing.
index_pos_controls: list of row indices in replicate_matrix corresponding to positive controls. index_neg_controls: list of row indices in replicate_matrix corresponding to negative controls.
- pyrnaither.stats.qc_todo.summarize_reps_no_filtering(data, col4val, col4anno)[source]
Summarize replicates without filtering.
- Return type:
DataFrame- Parameters:
data (DataFrame)
col4val (str)
col4anno (str)
- Args:
data: DataFrame containing at least columns [col4val, col4anno]. col4val: name of the intensity column to fetch when index_or_int=”Intensities”. col4anno: name of the annotation column grouping replicates.
- Returns:
DataFrame with col4val