preprocessing/regress_out
Description
Regress out (mostly) unwanted sources of variation.
Uses simple linear regression. This is a GPU-accelerated wrapper around
rapids_singlecell.pp.regress_out, taking the listed .obs columns as
covariates to regress out of the expression matrix.
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input -i | file required | Input h5mu file. |
--modality | string | Which modality from the input MuData file to process. |
--input_layer | string | Input layer to use. By default, X is used. |
--obs_keys | string required multiple | Keys of the .obs columns to regress out as covariates. |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output -o | file required output | Output h5mu file. |
--output_layer | string | Output layer to use. By default, use X. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied. |
Options
Name | Type & Properties | Description |
|---|---|---|
--batchsize | integer | Number of genes per batch. If None, all genes are processed at once. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "rna" ]
output: "$id.$key.output"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline_rapids.git \
-revision v0.1.3 \
-main-script target/nextflow/preprocessing/regress_out/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
preprocessing/regress_outopenpipeline_rapids v0.1.3
Uses
0 relationships
No component dependencies found.