Filter features

A common task in bulk and single-cell analysis is to filter the data to include only informative features before downstream analysis. Feature here means the measurement of observation, like gene expression, protein expression etc.

There is no gold standard for what makes a feature informative or not, and ideal feature filtering criteria depend on your experimental design and research question, Connected Multiomics has a wide variety of flexible filtering options.

Filter features task can be invoked from any counts or single cell data node. The filter is applied to the values in the selected data node and the output is a filtered version of the input data node.

In the task dialog, select the filter option to activate the filter type and configure the filter, then click Finish to run.

Noise reduction filter

The Noise reduction filter lets you exclude features that meet specified descriptive statistics criteria.

Descriptive statistics you can choose are:

• Geometric mean

• Maximum

• Mean

• Median

• Minimum

• Sum

• Variance

• Value

For each of these you can choose to exclude features that are:

• <: less than

• <=: less than or equal to

• == equal to

• >: greater than

• >=: greater than or equal to

The threshold is set using the text box. The input must be a number; it can be an integer or decimal, positive or negative.

If you select value, you can also choose a percentage of samples or cells that must meet the criteria for the feature to be excluded.

Statistics based filter

The Statistics based filter lets you include a number or percentile of features based on descriptive statistics.

Select Counts to specify a number of top features to include or select Percentiles to specify the top percentile of features to include.

Descriptive statistics you can choose are:

• Coefficient of variance

• Geometric mean

• Maximum

• Mean

• Median

• Minimum

• Range

• Standard deviation (std dev)

• Sum

• Variance

• Dispersion

Feature metadata filter

If the data linked to feature (gene) annotation, different fields in the annotation can be used to filter, e.g. genomic location information, gene biotype information etc.

You can specify "AND" "OR" logical operation using different annotation field information.

Saved list filter

You can filter features based on a feature lists.

You should have a saved list in the List management page when you use this option. Choose a feature list name from the drop-down menu which displays all the feature lists added in List management.

You can choose to include or exclude features in any list that you have added.

Use the Feature identifier option to choose which identifier from your annotation matches the values in the feature list.

Manual list filter

This option allows you to type in or paste a list of features, the delimiter should be commas or new lines between the feature names.

This task will generate a filtered counts data node which contains all the samples/cells from the input data but only the features meet the criteria.