GenePattern Module: spatialGE.Preprocessing
Description
The spatialGE.Preprocessing module is part of the spatialGE package, designed for preprocessing and initial data preparation of spatially-resolved transcriptomic data. It performs data ingestion, filtering, transformation, and pseudobulk operations to prepare data for downstream analysis in platforms such as GeoMx, Visium, and CosMx-SMI. Covers the steps up to transform_data in the spatialGE Basic functions vignette.
Module Details
- Input Data Archive:
- Input data archive in gz format. Should match the directory structure as defined by spatialGE.
- Input Clinical Data:
- Metadata associated with each sample in a csv file. The sample names must match the names of the folders containing the data.
Output Files
- Output Files:
- RDS file containing the filtered/transformed STList object for further processing. Also outputs various images including distribution plots before and after filtering, and pseudobulk PCA plot and heatmap.
Parameters
Filtering Parameters
| Name |
Description |
Default Value |
Type |
filter data |
Perform data filtering. |
True |
String |
Spot Filtering
| Name |
Description |
Default Value |
Type |
spot min reads |
The minimum number of total reads for a spot to be retained. |
5000 |
Integer |
spot max reads |
The maximum number of total reads for a spot to be retained. |
15000 |
Integer |
spot min genes |
The minimum number of non-zero counts for a spot to be retained. |
1000 |
Integer |
spot max genes |
The maximum number of non-zero counts for a spot to be retained. |
1000 |
Integer |
spot min percent |
The minimum percentage of counts for features defined by spot_pct_expr for a spot to be retained. |
0 |
Integer |
spot max percent |
The maximum percentage of counts for features defined by spot_pct_expr for a spot to be retained. |
|
Integer |
Gene Filtering
| Name |
Description |
Default Value |
Type |
gene min reads |
The minimum number of total reads for a gene to be retained. |
0 |
Integer |
gene max reads |
The maximum number of total reads for a gene to be retained. |
|
Integer |
gene min spots |
The minimum number of spots with non-zero counts for a gene to be retained. |
0 |
Integer |
gene max spots |
The maximum number of spots with non-zero counts for a gene to be retained. |
|
Integer |
gene min percent |
The minimum percentage of spots with non-zero counts for a gene to be retained. |
0 |
Integer |
gene max percent |
The maximum percentage of spots with non-zero counts for a gene to be retained. |
|
Integer |
Other Filtering
| Name |
Description |
Default Value |
Type |
filter samples |
Samples (as in names(x@counts)) to perform filtering. |
|
String |
rm tissue |
Sample (as in names(x@counts)) to remove from STlist. |
|
String |
rm spots |
Vector of spot/cell IDs to remove. |
|
String |
rm genes |
Vector of gene names to remove from STlist. |
|
String |
rm genes regex |
A regular expression that matches genes to remove. |
|
String |
spot percentage genes regex |
An expression to use with spot_minpct and spot_maxpct. By default ‘^MT-‘. |
|
Integer |
Pseudobulk Parameters
| Name |
Description |
Default Value |
Type |
pseudobulk |
Perform pseudobulk analysis (combining counts from each sample) and perform PCA. |
False |
String |
pseudobulk max var genes |
The number of most variable genes (standard deviation) to use in pseudobulk analysis. |
5000 |
Integer |
pseudobulk plot meta |
Name of the variable in the sample metadata to color points in the PCA plot. |
patient_id |
String |
pseudobulk heatmap num displayed genes |
The number of genes to display in the pseudobulk heatmap. |
30 |
Integer |
| Name |
Description |
Default Value |
Type |
transform data |
Type of data transformation to apply (None, Log, SCT). |
None |
String |
transform scale f |
The scale factor used in logarithmic transformation. |
10000 |
Integer |
transform num regression genes |
The number of genes to be used in the regression model during SCTransform. |
5000 |
Integer |
transform min spots or cells |
The minimum number of spots or cells to be used in the regression model fit by SCTransform. |
5 |
Integer |
Other Parameters
| Name |
Description |
Default Value |
Type |
verbose |
Output additional files including summarized STList, distribution_plots before and after filtering, and pseudobulk PCA plot and heatmap. |
- |
Integer |
distribution plot meta |
Vector of variables in sample metadata to plot distributions. |
- |
Integer |
Example Data
Example data on GitHub
License
spatialGE.Preprocessing is distributed under a modified BSD license available at [https://github.com/genepattern/ExampleModule/blob/v2/LICENSE](https://github.com/genepattern/spatialGE.Preprocessing/blob/main/LICENSE).
| Version |
Release Date |
Description |
| 1.1 |
August 6, 2024 |
Formatting updates. |
| 1 |
July 2, 2024 |
Initial version for team use. |