inst/script/exampleData.R

In haowulab/TRESS: Toolbox for mRNA epigenetics sequencing analysis

#### here is a simple pipeline of how to generate data saved in "inst/extdata/"

## Take bam files in datasetTRES
IP.file = c("cb_ip_rep1_chr19.bam", "cb_ip_rep2_chr19.bam")
Input.file = c("cb_input_rep1_chr19.bam", "cb_input_rep2_chr19.bam")
BamDir = file.path(system.file(package = "datasetTRES"), "extdata/")
OutDir = "/Users/zhenxingguo/Documents/research/m6a/packagetest"
TRESS_peak(IP.file = IP.file,
           Input.file = Input.file,
           Path_To_AnnoSqlite = annoDir,
           InputDir = BamDir,
           OutputDir = OutDir,
           experiment_name = "examplebyBam",
           filetype = "bam")
peaks = read.table(paste0(OutDir, "/examplebyBam_peaks.xls"), sep = "\t", header = TRUE)
head(peaks)