Nothing
## ----wrap-hook, echo=FALSE-----------------------------------------------
library(knitr)
opts_chunk$set(tidy.opts=list(width.cutoff=60),tidy=TRUE)
def.chunk.hook <- knitr::knit_hooks$get("chunk")
knitr::knit_hooks$set(chunk = function(x, options) {
x <- def.chunk.hook(x, options)
ifelse(options$size != "normalsize", paste0("\n \\", options$size,"\n\n", x, "\n\n \\normalsize"), x)
})
## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----eval=FALSE----------------------------------------------------------
# library(devtools)
# install_github("wenweixiong/VALERIE")
## ----message=FALSE, warning=FALSE----------------------------------------
library(VALERIE)
## ----message=FALSE, warning=FALSE, size="tiny"---------------------------
# Exon file (General)
exon.info <- read.table(system.file("extdata/Exon_Info", "Exon_Info_Further_Examples.txt", package="VALERIE"), sep="\t", header=FALSE, stringsAsFactors=FALSE)
print(exon.info)
# Exon file (Use for this example)
exon.info <- read.table(system.file("extdata/Exon_Info", "Exon_Info.txt", package="VALERIE"), sep="\t", header=FALSE, stringsAsFactors=FALSE)
print(exon.info)
# Sample information file
sample.info <- read.table(system.file("extdata/Sample_Info", "Sample_Info.txt", package="VALERIE"), sep="\t", header=FALSE, stringsAsFactors=FALSE)
head(sample.info) ; tail(sample.info)
# BAM files
BAM <- system.file("extdata/BAM", "", package="VALERIE")
head(list.files(BAM))
## ----eval=FALSE----------------------------------------------------------
# # Compute PSI
# PSI <- ComputePSI(SampleInfo=system.file("extdata/Sample_Info", "Sample_Info.txt", package="VALERIE"), ExonInfo=system.file("extdata/Exon_Info", "Exon_Info.txt", package="VALERIE"), BAM=system.file("extdata/BAM", "", package="VALERIE"), MinCoverage=10)
#
# # Plot PSI (Output as shown in Figure 1)
# PlotPSI(object=PSI, SampleInfo=system.file("extdata/Sample_Info", "Sample_Info.txt", package="VALERIE"), ExonInfo=system.file("extdata/Exon_Info", "Exon_Info.txt", package="VALERIE"), statistical.test="wilcox", multiple.testing="bonferroni", Plots=tempdir(), plot.width=5, plot.height=8, EventType="SE", Groups=2)
## ----message=FALSE-------------------------------------------------------
# Check plot
output <- system.file("extdata/Plots", "1_SE_Plots_Mbp.pdf", package="VALERIE")
knitr::include_graphics(output)
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