## ---- echo=FALSE--------------------------------------------------------------
htmltools::img(
    src = knitr::image_uri("magpie_hex.png"),
    alt = "logo",
    style = "position:absolute; top:0; left:0; padding:10px; height:280px"
)

## ---- eval = FALSE, warning=FALSE, message=FALSE------------------------------
#  install.packages("devtools") # if you have not installed "devtools" package
#  library(devtools)
#  install_github("https://github.com/dxd429/magpie",
#      build_vignettes = TRUE
#  )

## ---- eval = FALSE, warning=FALSE, message=FALSE------------------------------
#  if (!requireNamespace("BiocManager", quietly = TRUE)) {
#      install.packages("BiocManager")
#  }
#  BiocManager::install("magpie")

## ----eval=FALSE,warning=FALSE,message=FALSE-----------------------------------
#  library(magpie)
#  vignette("magpie")

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
library(magpie)
power.test <- quickPower(dataset = "GSE46705") # Options are 'GSE46705', 'GSE55575', and 'GSE94613'.

## ---- eval=FALSE, message=FALSE, warning=FALSE--------------------------------
#  ### write out .xlsx
#  writeToxlsx(power.test, file = "test_TRESS.xlsx")
#  
#  ### write out stratified results
#  writeToxlsx_strata(power.test, file = "test_strata_TRESS.xlsx")

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
### plot FDR under sequencing depth 1x
plotRes(power.test, depth_factor = 1, value_option = "FDR")

### plot all in a panel under sequencing depth 1x
plotAll(power.test, depth_factor = 1)

### plot a FDR strata result
plotStrata(power.test, value_option = "FDR")

### plot all strata results in a panel
plotAll_Strata(power.test)

## ---- eval= FALSE-------------------------------------------------------------
#  install.packages("devtools") # if you have not installed "devtools" package
#  library(devtools)
#  install_github("https://github.com/dxd429/magpieData",
#      build_vignettes = TRUE
#  )

## ---- eval=FALSE, message=FALSE, warning=FALSE--------------------------------
#  ## Use "makeTxDbFromUCSC" function to create an annotation file of hg18
#  library(GenomicFeatures)
#  hg18 <- makeTxDbFromUCSC(genome = "hg18", tablename = "knownGene")
#  saveDb(hg18, file = "hg18.sqlite")

## ---- eval=FALSE, message=FALSE, warning=FALSE--------------------------------
#  library(magpieData)
#  library(magpie)
#  ### Get the example data
#  BAM_path <- getBAMpath()
#  ### Call powerEval()
#  power.test <- powerEval(
#      Input.file = c("Ctrl1.chr15.input.bam", "Ctrl2.chr15.input.bam", "Case1.chr15.input.bam", "Case2.chr15.input.bam"),
#      IP.file = c("Ctrl1.chr15.ip.bam", "Ctrl2.chr15.ip.bam", "Case1.chr15.ip.bam", "Case2.chr15.ip.bam"),
#      BamDir = BAM_path,
#      annoDir = paste0(BAM_path, "/hg18_chr15.sqlite"),
#      variable = rep(c("Ctrl", "Trt"), each = 2),
#      bam_factor = 0.03,
#      nsim = 10,
#      N.reps = c(2, 3, 5, 7),
#      depth_factor = c(1, 2),
#      thres = c(0.01, 0.05, 0.1),
#      Test_method = "TRESS" ## TRESS or exomePeak2
#  )

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
library(magpie)
power.test <- quickPower(dataset = "GSE46705")

## ---- eval=FALSE, message=FALSE, warning=FALSE--------------------------------
#  ### write out .xlsx
#  writeToxlsx(power.test, file = "test_TRESS.xlsx")
#  
#  ### write out stratified results
#  writeToxlsx_strata(power.test, file = "test_strata_TRESS.xlsx")

## ---- echo=FALSE--------------------------------------------------------------
tb1 <- data.frame(
    FDR = rep("", 4),
    N_rep = c(2, 3, 5, 7),
    s0.01 = c(0.36, 0.14, 0.06, 0.04),
    s0.05 = c(0.48, 0.27, 0.13, 0.11),
    s0.1 = c(0.57, 0.38, 0.21, 0.17)
)
names(tb1) <- c("FDR", "N.rep", "0.01", "0.05", "0.1")
kableExtra::kable_styling(kableExtra::kable(tb1, align = "l"), latex_options = "HOLD_position")

## ---- echo=FALSE--------------------------------------------------------------
tb2 <- data.frame(
    FDR = rep("", 4),
    N_rep = c(2, 3, 5, 7),
    s1 = c(0.41, 0.23, 0.15, 0.12),
    s2 = c(0.46, 0.30, 0.16, 0.14),
    s3 = c(0.47, 0.27, 0.11, 0.08),
    s4 = c(0.58, 0.28, 0.12, 0.11)
)
names(tb2) <- c("FDR", "N.rep", "(0, 27.68]", "(27.68, 54.3]", "(54.3, 92.64]", "(92.64, Inf]")
kableExtra::kable_styling(knitr::kable(tb2, align = "l"), latex_options = "HOLD_position")

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------

### plot FDR under sequencing depth 1x
plotRes(power.test, depth_factor = 1, value_option = "FDR")

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
### plot all in a panel under sequencing depth 1x
plotAll(power.test, depth_factor = 1)

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
### plot a FDR strata result
plotStrata(power.test, value_option = "FDR")

## ---- eval=TRUE, message=FALSE, warning=FALSE---------------------------------
### plot all strata results in a panel
plotAll_Strata(power.test)

## ----sessionInfo, echo=FALSE--------------------------------------------------
sessionInfo()