quick_mode (run entire pipeline)

usage: gsmap quick_mode [-h] --workdir WORKDIR --sample_name SAMPLE_NAME
                        --gsMap_resource_dir GSMAP_RESOURCE_DIR --hdf5_path
                        HDF5_PATH --annotation ANNOTATION --data_layer
                        DATA_LAYER [--trait_name TRAIT_NAME]
                        [--sumstats_file SUMSTATS_FILE]
                        [--sumstats_config_file SUMSTATS_CONFIG_FILE]
                        [--homolog_file HOMOLOG_FILE]
                        [--max_processes MAX_PROCESSES]
                        [--latent_representation LATENT_REPRESENTATION]
                        [--num_neighbour NUM_NEIGHBOUR]
                        [--num_neighbour_spatial NUM_NEIGHBOUR_SPATIAL]
                        [--gM_slices GM_SLICES]

Named Arguments

--workdir

Path to the working directory.

--sample_name

Name of the sample.

--gsMap_resource_dir

Directory containing gsMap resources (e.g., genome annotations, LD reference panel, etc.).

--hdf5_path

Path to the input spatial transcriptomics data (H5AD format).

--annotation

Name of the annotation in adata.obs to use.

--data_layer

Data layer for gene expression (e.g., “count”, “counts”, “log1p”).

Default: 'counts'

--trait_name

Name of the trait for GWAS analysis (required if sumstats_file is provided).

--sumstats_file

Path to GWAS summary statistics file. Either sumstats_file or sumstats_config_file is required.

--sumstats_config_file

Path to GWAS summary statistics config file. Either sumstats_file or sumstats_config_file is required.

--homolog_file

Path to homologous gene for converting gene names from different species to human (optional, used for cross-species analysis).

--max_processes

Maximum number of processes for parallel execution.

Default: 10

--latent_representation

Type of latent representation. This should exist in the h5ad obsm.

--num_neighbour

Number of neighbors.

Default: 21

--num_neighbour_spatial

Number of spatial neighbors.

Default: 101

--gM_slices

Path to the slice mean file (optional).