transform/regress_out
Description
Regress out (mostly) unwanted sources of variation.
Uses simple linear regression. This is inspired by Seurat's regressOut function in R [Satija15].
Note that this function tends to overcorrect in certain circumstances as described in issue theislab/scanpy#526.
See https://github.com/theislab/scanpy/issues/526.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input h5mu file |
--output -o | file required output | Output h5mu file. |
--modality | string | Which modality (one or more) to run this component on. |
--obs_keys | string multiple | Which .obs keys to regress on. |
--input_layer | string | The layer of the adata object to regress on. If not provided, the X attribute of the adata object will be used. |
--output_layer | string | The layer of the adata object containing the regressed count data. If not provided, the X attribute of the adata object will be used. |
--output_compression | string | Compression format to use for the output AnnData and/or Mudata H5 files. By default no compression is applied. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
output: "$id.$key.output"
modality: [ "rna" ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision v4.1.0 \
-main-script target/nextflow/transform/regress_out/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
transform/regress_outopenpipeline v4.1.0
Uses
0 relationships
No component dependencies found.