An R package for single-cell eQTL analysis and visualization

---

Documentation for package ‘scQTLtools’ version 1.0.2

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

adjust_pvalues	Adjust p-values and filter gene-SNP pairs based on the adjusted p-values.
buildZINB	Build a ZINB model.
callQTL	Identify single-cell eQTLs exclusively using scRNA-seq data.
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	Test Gene Expression Dataset
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' The eQTLObject class is designed to store data related to eQTL analysis, including data lists, result data frames, and additional metadata such as classification, species, and grouping information.
filterGeneSNP	Filter gene expression and genotype matrices by cell percentage thresholds.
filter_by_abs_b	Filter a data frame of gene–SNP pairs by absolute beta.
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.
show-method	Show Method for eQTLObject Class
testEQTL	Test Gene Expression Dataset
testGene	Test Gene Expression Dataset
testSeurat	Test Gene Expression Dataset
testSNP	Test Gene Expression Dataset
testSNP2	Test Gene Expression Dataset
TPM_normalize	Normalize the gene expression matrix with TPM
visualizeQTL	Visualize eQTL results by gene-SNP pair across groups
zinbModel	Zinb model fitting the gene expression matrix.