An R package for single-cell eQTL analysis and visualization

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Documentation for package ‘scQTLtools’ version 0.99.11

• 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.