| adjust_pvalues | Adjust p-values and perform threshold filtering based on the adjusted p-values. |
| buildZINB | Build zinb model. |
| callQTL | callQTL: Uncover single-cell eQTLs exclusively using scRNA-seq data. A function designed to identify eQTLs from scRNA-seq data. |
| checkSNPList | Check if the SNP ids in the input genotype matrix are valid. |
| CPM_normalize | Normalize the gene expression matrix with CPM. |
| createGeneLoc | Create gene location dataframe. |
| createQTLObject | createObject:Create the eQTLObject. We next create a S4 object. The object serves as a container that contains both data (like the count matrix) and meta.data. |
| createSNPsLoc | Create SNP location dataframe. |
| DESeq_normalize | Normalize the gene expression matrix with DESeq. |
| draw_boxplot | Generate a boxplot of expression levels by SNP factor |
| draw_histplot | Generate a hist plot of expression levels by SNP factor. |
| draw_QTLplot | Create a combined plot with violin, boxplot, and scatter point overlay. |
| draw_violinplot | Generate a violin plot of expression levels by SNP factor |
| eQTLObject-class | Class 'eQTLObject' The eQTLObject class is an R object designed to store data related to eQTL analysis, encompassing data lists, result data frames, and layers for biClassify, species, and grouping information. |
| filterGeneSNP | filterGeneSNP: Filter gene expression matrix and genotype matrix. |
| filter_by_abs_b | Filters data frame by absolute b-values, returning rows meeting or exceeding a threshold. |
| get_cell_groups | Retrieve Cells by SNP Value |
| get_counts | Extract Counts from an Expression Matrix |
| get_filter_data | Generic to access eQTLObject filter data |
| get_filter_data-method | Method to access eQTLObject filter data |
| get_model_info | Generic to access eQTLObject used model information |
| get_model_info-method | Method to access eQTLObject used model information |
| get_raw_data | Generic to access eQTLObject raw data |
| get_raw_data-method | Method to access eQTLObject raw data |
| get_result_info | Generic to access the result of identifying eQTLs from scRNA-seq data |
| get_result_info-method | Method to access the result of identifying eQTLs from scRNA-seq data |
| initialize_progress_bar | Progress Bar for Model Analysis. |
| limma_normalize | Normalize the gene expression matrix with limma |
| linearModel | Linear model fitting the gene expression matrix and genotype matrix. |
| load_biclassify_info | Generic to access eQTLObject biclassify information |
| load_biclassify_info-method | Method to access eQTLObject biclassify information |
| load_group_info | Generic to access eQTLObject cell grouping information |
| load_group_info-method | Method to access eQTLObject cell grouping information |
| load_species_info | Generic to access eQTLObject species information |
| load_species_info-method | Method to access eQTLObject species information |
| log_normalize | Normalize the gene expression matrix with logNormalize method. |
| normalizeGene | normalizeGene: Normalize the gene expression data. |
| plots_theme_opts | Theme options for customized plots |
| poissonModel | Poisson model fitting the gene expression matrix and genotype matrix. |
| process_matrix | Process a matrix to extract a row and convert it to a data frame |
| remove_outliers | Remove outliers from gene expression data and update cell lists |
| set_filter_data | Generic to set eQTLObject filter data |
| set_filter_data-method | Method to set eQTLObject filter data |
| set_model_info | Generic to set eQTLObject used model information |
| set_model_info-method | Method to set eQTLObject used model information |
| set_raw_data | Generic to set eQTLObject raw data |
| set_raw_data-method | Method to set eQTLObject raw data |
| set_result_info | Generic to set the result of identifying eQTLs from scRNA-seq data |
| set_result_info-method | Method to set the result of identifying eQTLs from scRNA-seq data |
| show-method | Show Method for eQTLObject Class |
| testEQTL | Test eqtl object |
| testGene | Test Gene Expression Dataset |
| testSeurat | Test SeuratObject |
| testSNP | Test Genotype Dataset |
| testSNP2 | Test Genotype Dataset |
| TPM_normalize | Normalize the gene expression matrix with TPM |
| visualizeQTL | visualizeQTL: Visualize the gene-snp pairs by group. |
| zinbModel | Zinb model fitting the gene expression matrix. |