modules/custom_matrixfilter

Groovy Map containing information on matrix to be filtered, at a
minimum an id. e.g. [ id:‘test’ ]

Raw TSV or CSV format abundance matrix with features (e.g.
genes) by row and observations (e.g. samples) by column. All rownames
from the sample sheet should be present in the columns.

Where samplesheet is provided, aroovy Map containing information on
sample sheet, at a minimum an id. e.g. [ id:‘test’ ]

Optional CSV or TSV format sample sheet with sample metadata. If
provided this is used to infer minimum passing samples from group sizes
present (see grouping_variable), but also to validate matrix columns.
If not provided, all numeric columns are selected.

Minimum abundance value, supplied via task.ext.args as —minimum_abundance

Minimum observations that must pass the threshold to retain
the row/ feature (e.g. gene). Supplied via task.ext.args as
—minimum_samples

A minimum proportion of observations that must pass the threshold.
Supplied via task.ext.args as —minimum_proportion. Overrides
minimum_samples

Optionally supply a variable from the sample sheet that can be used to
define groups and derive a minimum group size upon which to base
minimum observation numbers. The rationale being to allow retention of
features that might be present in only one group. Supplied via
task.ext.args as —grouping_variable

A minimum proportion of observations that must have a numeric value (not be NA).
Supplied via task.ext.args as —minimum_proportion_not_na

Minimum observations that must have a numeric value (not be NA) to retain
the row/ feature (e.g. gene). Supplied via task.ext.args as
—minimum_samples_not_na. Overrides minimum_proportion_not_na

Variance filter for the number of row/ feature (e.g. gene) observations returned.
Supplied via task.ext.args as —most_variant_features