Dropping Entries from Datasets

This module provides the functionality to drop sets of entries from the annotation and expression matrix.

Warning

Depending on the size of the expression matrix, this can be very memory consuming! If working on a cluster, make sure to use a node with enough memory.

Usage

>>> eco_helper drop [--samples <samples>] [--celltypes <celltypes>] [--ids <ids>] <annotation> <expression>

where <annotation> and <expression> are an annotation and expression matrix file for Ecotyper. The --samples option allows to drop entries belonging to specific samples from the dataset (as given by the Sample column in the annotation file). The --celltypes option allows to drop entries belonging to specific cell types from the dataset (as given by the CellType column in the annotation file). The --ids option allows to drop specific entries from the dataset (as given by the ID column in the annotation file). The --samples, --celltypes and --ids may be provided together.

Full CLI

usage: eco_helper drop [-h] [-o OUTPUT] [-s SAMPLES [SAMPLES ...]] [-c CELLTYPES [CELLTYPES ...]] [-i IDS [IDS ...]] [-scol SAMPLECOL] [-ccol CELLTYPECOL]
                   [-idcol IDCOL]
                   annotation expression

This command allows removal of entries from EcoTyper datasets.

positional arguments:
annotation            The file storing the annotations.
expression            The file storing the expression matrix.

options:
-h, --help            show this help message and exit
-o OUTPUT, --output OUTPUT
                        The output basename. This will generate a <basename>.annotation.tsv and <basename>.expression.tsv file. By default, the input filenames are
                        appended by '.drop' at the end.
-s SAMPLES [SAMPLES ...], --samples SAMPLES [SAMPLES ...]
                        The samples whose entries to drop
-c CELLTYPES [CELLTYPES ...], --celltypes CELLTYPES [CELLTYPES ...]
                        The cell-types whose entries to drop
-i IDS [IDS ...], --ids IDS [IDS ...]
                        Specific entries to drop
-scol SAMPLECOL, --samplecol SAMPLECOL
                        The column containing the sample annotations. By default EcoTyper-friendly 'Sample' is assumed.
-ccol CELLTYPECOL, --celltypecol CELLTYPECOL
                        The column containing the cell-type annotations. By default EcoTyper-friendly 'CellType' is assumed.
-icol IDCOL, --idcol IDCOL
                        The column containing the entry identifiers. By default EcoTyper-friendly 'ID' is assumed.

eco_helper.drop.funcs module

These are the main functions that are used by eco_helper drop.

eco_helper.drop.funcs.drop_celltypes(dataset: Dataset, celltypes: list) → Dataset

Drop celltypes from the dataset.

Parameters

  • dataset (Dataset) – The dataset to drop samples from.

  • celltypes (list) – The celltypes to drop.

Returns

The dataset with the cropped dataset.

Return type

Dataset

eco_helper.drop.funcs.drop_from_col(dataset: Dataset, values: list, col: str) → Dataset

Drop entries from the dataset using some column.

Parameters

  • dataset (Dataset) – The dataset to drop samples from.

  • values (list) – The entries belonging to these values should be dropped.

  • col (str) – The column to use for dropping.

Returns

The dataset with the cropped dataset.

Return type

Dataset

eco_helper.drop.funcs.drop_ids(dataset: Dataset, ids: list) → Dataset

Drop entries from the dataset.

Parameters

  • dataset (Dataset) – The dataset to drop samples from.

  • ids (list) – The IDs to drop.

Returns

The dataset with the cropped dataset.

Return type

Dataset

eco_helper.drop.funcs.drop_samples(dataset: Dataset, samples: list) → Dataset

Drop samples from the dataset.

Parameters

  • dataset (Dataset) – The dataset to drop samples from.

  • samples (list) – The samples to drop.

Returns

The dataset with the cropped dataset.

Return type

Dataset