# An R package for single-cell eQTL analysis and visualization

## Documentation for package ‘scQTLtools’ version 1.0.0

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

## Help Pages

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.