DataSet

Constructor

class itpseq.DataSet(data=None, *, data_path: Path | None = None, result_path: Path | None = None, samples: dict | None = None, keys=None, ref_labels: str | tuple | None = 'noa', cache_path=None, file_pattern=None, allow_partial_keys=True, ref_mapping=None)

Attributes:

samples_with_ref

Methods

DE([pos])	Computes the log2-FoldChange for each motif described by pos for each sample in the DataSet relative to their reference
infos([html])	Displays summary information about the dataset NGS reads per replicate.
itoeprint([plot, norm, norm_range, ...])	Plots a virtual inverse-toeprint gel.
itp_len_plot([ax, col, row, min_codon, ...])	Generates a line plot of inverse-toeprint (ITP) counts per length.
reorder_samples(order[, validate, ...])	Reorders the samples in the DataSet.
report([template, output])	Create a report for the DataSet.

set_references

Methods

DataSet.reorder_samples(order[, validate, ...])	Reorders the samples in the DataSet.
DataSet.infos([html])	Displays summary information about the dataset NGS reads per replicate.
DataSet.DE([pos])	Computes the log2-FoldChange for each motif described by pos for each sample in the DataSet relative to their reference
DataSet.itp_len_plot([ax, col, row, ...])	Generates a line plot of inverse-toeprint (ITP) counts per length.
DataSet.report([template, output])	Create a report for the DataSet.
DataSet.itoeprint([plot, norm, norm_range, ...])	Plots a virtual inverse-toeprint gel.