# scQTLtools: an R/Bioconductor package for comprehensive identification and visualization of single-cell eQTLs

## Documentation for package ‘scQTLtools’ version 1.4.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

adjust_pvalues | Adjust p-values and filter SNP–gene pairs based on the adjusted p-values.
buildZINB | Build a ZINB model.
callQTL | Identify single-cell eQTLs.
checkSNPList | Validate SNP IDs in the input genotype matrix.
CPM_normalize | Normalize gene expression using CPM.
createGeneLoc | Create a gene location data frame.
createQTLObject | Create an eQTLObject for storing sc-eQTL analysis data.
createSNPsLoc | Create SNP location dataframe.
DataSet | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
DESeq_normalize | Normalize the gene expression matrix with DESeq2.
draw_boxplot | Generate a boxplot of gene expression by SNP genotype.
draw_histplot | Generate a histogram of gene expression by SNP genotype.
draw_QTLplot | Create a combined violin-box-scatter plot.
draw_violinplot | Generate a violin plot of gene expression by SNP genotype.
eQTLObject-class | Class 'eQTLObject'
EQTL_obj | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
filterGeneSNP | Filter gene expression and genotype matrices by cell percentage thresholds.
filter_by_abs_b | Filter a data frame of SNP–gene pairs by absolute beta.
GeneData | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
get_cell_groups | Retrieve Cells by SNP Value
get_counts | Extract Counts from an Expression Matrix
get_filter_data | Access filtered data stored in an eQTLObject.
get_filter_data-method | Access filtered data stored in an eQTLObject.
get_model_info | Access model specification from an eQTLObject
get_model_info-method | Access model specification from an eQTLObject
get_raw_data | Access raw data stored in an eQTLObject.
get_raw_data-method | Access raw data stored in an eQTLObject.
get_result_info | Access eQTLs results from an eQTLObject.
get_result_info-method | Access eQTLs results from an eQTLObject.
initialize_progress_bar | Progress Bar for Model Analysis.
limma_normalize | Normalize the gene expression matrix with limma
linearModel | Fit Linear Model for eQTL Mapping
load_biclassify_info | Access biclassification information from an eQTLObject.
load_biclassify_info-method | Access biclassification information from an eQTLObject.
load_group_info | Access cell grouping information from an eQTLObject
load_group_info-method | Access cell grouping information from an eQTLObject
load_species_info | Access species information from an eQTLObject.
load_species_info-method | Access species information from an eQTLObject.
log_normalize | Normalize the gene expression matrix with logNormalize method.
normalizeGene | Normalize gene expression data.
plots_theme_opts | Customized ggplot2 Theme for 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 groups.
set_filter_data | Set filtered data in an eQTLObject.
set_filter_data-method | Set filtered data in an eQTLObject.
set_model_info | Set model specification in an eQTLObject
set_model_info-method | Set model specification in an eQTLObject
set_raw_data | Set raw data in an eQTLObject.
set_raw_data-method | Set raw data in an eQTLObject.
set_result_info | Set eQTL results in an eQTLObject.
set_result_info-method | Set eQTL results in an eQTLObject.
Seurat_obj | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
SNPData | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
SNPData2 | The package includes five examplt datasets: a gene expression matrix, two SNP genotype matrices, a Seurat object, and an eQTL object.
TPM_normalize | Normalize the gene expression matrix with TPM
visualizeQTL | Visualize eQTL results by SNP–gene pair across groups
zinbModel | Zinb model fitting the gene expression matrix.