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. |