### scGWAS Essential Parameters for Quick Start Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Lists the minimum required parameters for running scGWAS, which users must provide even if other parameters can use default values. ```APIDOC Essential Parameters: - gwas_node_file - scrn_expr_file - network_file - outfile Note: It is suggested to use the full path to each input file due to potential Java file lookup issues. ``` -------------------------------- ### Run scGWAS Analysis with Java Source: https://github.com/bsml320/scgwas/blob/main/example/example.README.md This command executes the scGWAS analysis using the provided configuration file. It requires the scGWAS_v4.jar executable and a pre-configured input file. The analysis will generate three output files upon completion. ```Java java -jar scGWAS_v4.jar configure.Schizophrenia_Pardinas_2018.DER22.txt ``` -------------------------------- ### scGWAS Configuration File Rules Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Defines the general syntax and rules for the scGWAS configuration file, including parameter formatting, case sensitivity, and file naming conventions. ```APIDOC Parameter Format: - One parameter per row - Case sensitive: all parameters and their values are case sensitive (e.g., 'permutation=true' vs 'permutation=True'). Logical values 'true' and 'false' must be lower case. - No space: File names of input files should not contain spaces. - Format: keyword=value (e.g., 'r_include=0.1') ``` -------------------------------- ### scGWAS Parameter: outfile Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Defines the output folder where all results and intermediate files will be saved, requiring pre-creation. ```APIDOC outfile: Type: folder name Description: The folder name (not a file name) where the output files (as well as intermediate files) will be saved. This folder should be created before running scGWAS. ``` -------------------------------- ### scGWAS Model Running Parameters: r_include, r_exclude, remove_zero Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Parameters related to model execution, generally recommended to be left at their suggested default values. ```APIDOC r_include: Type: float Suggested Value: 0.1 Description: Parameter for model running. r_exclude: Type: float Suggested Value: 0.05 Description: Parameter for model running. remove_zero: Type: boolean Suggested Value: true Description: Parameter for model running. ``` -------------------------------- ### Run scGWAS Java Package Source: https://github.com/bsml320/scgwas/blob/main/README.md Executes the scGWAS Java package from the command line. All operational parameters are passed to the JAR via a specified configuration file. Users must have a Java Running Environment set up. ```Shell java -jar scGWAS_r0.jar configure.txt ``` -------------------------------- ### scGWAS Parameter: run_model Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Specifies the model to be run, always set to 'node' for node-weighted module search. ```APIDOC run_model: Type: string Default: "node" Description: Indicates node-weighted module search. ``` -------------------------------- ### scGWAS Parameter: verbose Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Determines if intermediate results should be printed to the screen during execution. ```APIDOC verbose: Type: boolean Description: Whether to print the intermediate results on screen. ``` -------------------------------- ### scGWAS Parameter: permutation Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Controls whether the virtual search process (permutation) should be conducted. ```APIDOC permutation: Type: boolean Suggestion: true Description: Whether to conduct the virtual search process or not. ``` -------------------------------- ### scGWAS Parameter: normalization_model Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Defines the normalization strategy for the model. 'calibration' is the suggested and default value. ```APIDOC normalization_model: Type: string Default: "calibration" Available Values: "calibration", "scale" Suggestion: Always set as "calibration". ``` -------------------------------- ### scGWAS Parameter: module_num Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Sets the number of random modules to be generated for each size during the analysis. ```APIDOC module_num: Type: integer Default: 1000 Description: The number of random modules to be generated for each size. ``` -------------------------------- ### scGWAS Parameter: scrn_expr_file Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Defines the input file for cellular gene expression from scRNA-seq data, including format and specific requirements for gene inclusion. ```APIDOC scrn_expr_file: Type: file path Description: The file with cellular gene expression per cell type from scRNA-seq data. Format: - Each row: represents a gene. - Each column: represents one cell type. - Expression value: average log-transformed CPM for each gene in each cell type (average across all cells assigned to the corresponding cell type). Note: All genes that pass a pre-defined threshold (e.g., with the zero-value in <95% cells) should be included for the estimation of the null distribution, unlike typical scRNA-seq analyses where only highly variable genes are selected. ``` -------------------------------- ### scGWAS Parameter: module_score Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Determines the method for calculating the module score, with options 'penalty' and 'tw' corresponding to different formulas. ```APIDOC module_score: Type: string Default: "penalty" Available Values: "penalty", "tw" Description: - When "penalty": m = mg + mv - sd(mg, mv) - When "tw": m = mg + mv ``` -------------------------------- ### scGWAS Parameter: gwas_node_file Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Specifies the input file containing boxcox-transformed z-scores per gene from GWAS, detailing its format and content requirements. ```APIDOC gwas_node_file: Type: file path Description: The file with boxcox-transformed z-scores per gene from GWAS. Format: - Two-column, tab-separated file. - Column 1: gene symbol. - Column 2: z-score. - No header line. Note: Gene-based scores should be transformed to an approximate normal distribution (e.g., Box-Cox transformation). Users can map SNPs to genes using customized strategies (e.g., functional annotations, QTLs) and provide the resultant gene-based scores. ``` -------------------------------- ### scGWAS Parameter: network_file Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Specifies the file containing gene-gene relationships, typically from collections like PathwayCommons, with exclusions noted. ```APIDOC network_file: Type: file path Description: The file including gene-gene relationships. The PathwayCommons collection was used, containing various relationship types (e.g., catalysis, chemical effect, regulation of expression or phosphorylation, react, interacts-with). Format: - Each row: represents a pair of genes. Note: Interactions involving MHC genes have been excluded. ``` -------------------------------- ### scGWAS Parameter: exclude_genes_file Source: https://github.com/bsml320/scgwas/blob/main/analysis/explanation_configure.md Specifies a file listing genes to be excluded from the analysis, such as house-keeping genes. ```APIDOC exclude_genes_file: Type: file path Description: Genes in this file will be excluded from the analysis (e.g., those annotated as house-keeping genes). ``` === COMPLETE CONTENT === This response contains all available snippets from this library. No additional content exists. Do not make further requests.