## ----eval = FALSE-------------------------------------------------------------
# if (!require("BiocManager"))
#     install.packages("BiocManager")
# BiocManager::install("scQTLtools")

## ----input, message=FALSE-----------------------------------------------------
library(scQTLtools)
# gene expression matrix
data(testGene)
# SeuratObject
data(testSeurat)
# load the genotype data
data(testSNP)
data(testSNP2)

## ----createObject_matrix, message=FALSE---------------------------------------
eqtl_matrix <- createQTLObject(
    snpMatrix = testSNP,
    genedata = testGene,
    biClassify = FALSE,
    species = 'human',
    group = NULL)

## ----createObject_matrix_bi, message=FALSE------------------------------------
eqtl_matrix_bi <- createQTLObject(
    snpMatrix = testSNP,
    genedata = testGene,
    biClassify = TRUE,
    species = 'human',
    group = NULL)

## ----createObject_seuratobject, message=FALSE---------------------------------
eqtl_seurat <- createQTLObject(
    snpMatrix = testSNP2,
    genedata = testSeurat,
    biClassify = FALSE,
    species = 'human',
    group = "celltype")

## ----createObject_sceobject, message=FALSE------------------------------------
# create a sce
library(SingleCellExperiment)
sce <- SingleCellExperiment(assays = list(counts = testGene))
eqtl_sce <- createQTLObject(
    snpMatrix = testSNP,
    genedata = sce,
    biClassify = FALSE,
    species = 'human',
    group = NULL)

## ----Normalize_matrix, message=FALSE------------------------------------------
eqtl_matrix  <- normalizeGene(
    eQTLObject = eqtl_matrix, 
    method = "logNormalize")

## ----Normalize_sceobject, message=FALSE---------------------------------------
eqtl_sce  <- normalizeGene(
    eQTLObject = eqtl_sce, 
    method = "logNormalize")

## ----filter_matrix, message=FALSE---------------------------------------------
eqtl_matrix <- filterGeneSNP(
    eQTLObject = eqtl_matrix,
    snpNumOfCellsPercent = 2,
    expressionMin = 0,
    expressionNumOfCellsPercent = 2)

## ----filter_seuratobject, message=FALSE---------------------------------------
eqtl_seurat <- filterGeneSNP(
    eQTLObject = eqtl_seurat,
    snpNumOfCellsPercent = 2,
    expressionMin = 0,
    expressionNumOfCellsPercent = 2)

## ----filter_sceobject, message=FALSE------------------------------------------
eqtl_sce <- filterGeneSNP(
    eQTLObject = eqtl_sce,
    snpNumOfCellsPercent = 2,
    expressionMin = 0,
    expressionNumOfCellsPercent = 2)

## ----callQTL1_matrix, message=FALSE-------------------------------------------
eqtl1_matrix <- callQTL(
    eQTLObject = eqtl_matrix,
    gene_ids = NULL,
    downstream = NULL,
    upstream = NULL,
    gene_mart = NULL,
    snp_mart = NULL,
    pAdjustMethod = "bonferroni",
    useModel = "linear",
    pAdjustThreshold = 0.05,
    logfcThreshold = 0.1)

## ----callQTL1_seuratobject, message=FALSE-------------------------------------
eqtl1_seurat <- callQTL(
    eQTLObject = eqtl_seurat,
    gene_ids = NULL,
    downstream = NULL,
    upstream = NULL,
    gene_mart = NULL,
    snp_mart = NULL,
    pAdjustMethod = "bonferroni",
    useModel = "linear",
    pAdjustThreshold = 0.05,
    logfcThreshold = 0.025)

## ----callQTL1_sceobject, message=FALSE----------------------------------------
eqtl1_sce <- callQTL(
    eQTLObject = eqtl_sce,
    gene_ids = NULL,
    downstream = NULL,
    upstream = NULL,
    gene_mart = NULL,
    snp_mart = NULL,
    pAdjustMethod = "bonferroni",
    useModel = "linear",
    pAdjustThreshold = 0.05,
    logfcThreshold = 0.025)

## ----callQTL2_matrix, message=FALSE-------------------------------------------
eqtl2_matrix <- callQTL(
    eQTLObject = eqtl_matrix,
    gene_ids = c("CNN2", 
                "RNF113A", 
                "SH3GL1", 
                "INTS13", 
                "PLAU"),
    downstream = NULL,
    upstream = NULL,
    gene_mart = NULL,
    snp_mart = NULL,
    pAdjustMethod = "bonferroni",
    useModel = "poisson",
    pAdjustThreshold = 0.05,
    logfcThreshold = 0.1)

## ----callQTL3_matrix, message=FALSE-------------------------------------------
eqtl3_matrix <- callQTL(
    eQTLObject = eqtl_matrix,
    gene_ids = NULL,
    downstream = -9e7,
    upstream = 2e8,
    gene_mart = NULL,
    snp_mart = NULL,
    pAdjustMethod = "bonferroni",
    useModel = "poisson",
    pAdjustThreshold = 0.05,
    logfcThreshold = 0.05)

## ----visualizeQTL_matrix, message=FALSE---------------------------------------
visualizeQTL(
    eQTLObject = eqtl1_matrix,
    SNPid = "1:632647",
    Geneid = "RPS27",
    groupName = NULL,
    plottype = "QTLplot",
    removeoutlier = TRUE)

## ----visualizeQTL_seuratobject, message=FALSE---------------------------------
visualizeQTL(
    eQTLObject = eqtl1_seurat,
    SNPid = "1:632647",
    Geneid = "RPS27",
    groupName = NULL,
    plottype = "QTLplot",
    removeoutlier = TRUE)

## ----visualizeQTL_seuratobject_groupName, message=FALSE-----------------------
visualizeQTL(
    eQTLObject = eqtl1_seurat,
    SNPid = "1:632647",
    Geneid = "RPS27",
    groupName = "GMP",
    plottype = "QTLplot",
    removeoutlier = TRUE)

## ----visualizeQTL_sceobject, message=FALSE------------------------------------
visualizeQTL(
    eQTLObject = eqtl1_sce,
    SNPid = "1:632647",
    Geneid = "RPS27",
    groupName = NULL,
    plottype = "boxplot",
    removeoutlier = TRUE)

## -----------------------------------------------------------------------------
sessionInfo()