#'@title Produce code for Peak Calling with exomePeak2
#'@import magrittr
#'@import exomePeak2
#'@export
exomePeak2_hg19 <- function(
coldata,
bam_dir,
front_name,
single_base = FALSE,
GC_correct = TRUE,
correct_GC_bg = FALSE,
background = "Gaussian_mixture",
qtnorm = TRUE
) {
#Create specific representation of those code.
code_library <- c("library(exomePeak2)",
"library(TxDb.Hsapiens.UCSC.hg19.knownGene)",
"library(BSgenome.Hsapiens.UCSC.hg19)")
code_directory <- c(
paste0("dir.create('", front_name, coldata$Experiment[1], "')"),
paste0("setwd('", front_name, coldata$Experiment[1], "')" )
)
if(!single_base) {
code_annot <- "sb_gr = NULL"
}else{
code_annot <- 'sb_gr = readRDS(system.file("extdata", "m6A_hg19_annot.rds", package = "exomePeak2"))'
}
bam_files <- paste0( bam_dir, "/", coldata$SRR_RUN, ".bam" )
code_ep2 <- call("exomePeak2",
bam_ip = bam_files[coldata$IP_input == "IP"],
bam_input = bam_files[coldata$IP_input == "input"],
paired_end = all(coldata$Lib == "Paired"),
correct_GC_bg = correct_GC_bg,
background = background,
qtnorm = qtnorm,
export_format = "CSV",
save_plot_analysis = T
) %>% deparse
arguments_plot <- c( ifelse(GC_correct,"Hsapiens","NULL"),
"TxDb.Hsapiens.UCSC.hg19.knownGene",
"sb_gr" )
names(arguments_plot) <- c("bsgenome", "txdb", "mod_annot")
code_ep2 <- introduce_arg( code_ep2 , arguments_plot )
return(c(code_library, code_directory, code_annot, code_ep2))
}
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