This function filters genes from a `SummarizedExperiment` object based on minimum expression thresholds.
Arguments
- exp_data
A `SummarizedExperiment` object containing the gene expression data with a `counts` assay.
- min_nsamp
An integer specifying the minimum number of samples in which a gene must have expression above `min_counts` to be retained. Default is 1.
- min_counts
An integer specifying the minimum count threshold a gene must have in `min_nsamp` samples to be retained. Default is 10.
Value
A filtered `SummarizedExperiment` object containing only the genes that meet the specified criteria. Two new columns are added to `colData`: - `ncounts`: Total counts per sample. - `nfeats`: Number of features (genes) detected per sample.
Details
This function removes genes that do not meet the specified thresholds for expression. It adds sample-level metrics (`ncounts` and `nfeats`) to the `colData` of the `SummarizedExperiment` object for downstream analysis.
The filtering criteria are: - A gene must have expression greater than or equal to `min_counts` in at least `min_nsamp` samples.