--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/chipenrich.R	Thu May 20 08:41:45 2021 +0000
@@ -0,0 +1,141 @@
+###############################################################################
+# title: chipenrich
+# author: Xiaowei
+# time: Mar.31 2021
+###############################################################################
+
+spec <- matrix(c("input_peaks", "P",1, "character", "peaks file",
+                 "input_genome","G",1, "character", "genome",
+                 "input_locusdef","L",1,"character", "locusdef",
+                 "input_mappability","Map",0, "logical", "mappability",
+                 "input_qc_plot","Q",0, "logical", "qc_plot",
+                 "input_method","M",1,"character", "method",
+                 "input_geneset","GS",1,"character", "geneset_category",
+                 "input_minSize","Min",1,"integer","minSize",
+                 "input_maxSize","Max",1,"integer", "maxSize",
+                 "input_randomization","random",1,"character","randomization",
+                 "input_reglocation","reg",1,"character","reglocation",
+                 "input_num_peak_threshould","threshould",1,"numeric", "peak_threshould",
+                 "output_peaks","out_peaks",1,"character","output_peaks",
+                 "output_peaks_per_gene","out_ppg",1,"character","peaks per gene",
+                 "output_enrich_results","out_er",1,"character", "enrich result",
+                 "output_qc_plot", "out_qc", 1,"character","output_qc_plot"
+                 ),byrow = TRUE, ncol = 5)
+
+opt <- getopt::getopt(spec)
+
+
+#----------------------------------------------------------------
+
+input_peaks <- read.csv(opt$input_peaks,header = TRUE)
+input_genome = opt$input_genome
+input_locusdef = opt$input_locusdef
+
+if (!is.null(opt$input_mappability)){
+  input_mappability = 24 #根据表格来填写
+}else{
+  input_mappability = NULL #supported_read_lengths()
+}
+
+if(!is.null(opt$input_qc_plot)){
+  input_qc_plot = opt$input_qc_plot
+  input_output_name = "x"
+}else{
+    input_qc_plot = FALSE
+    input_output_name = NULL
+}
+
+
+if (!is.null(opt$input_method)){input_method = opt$input_method}else{input_method ="chipenrich"}
+if(!is.null(opt$input_geneset)){input_geneset = strsplit(opt$input_geneset, split = ",")[[1]]}else{input_geneset = NULL}
+if(!is.null(opt$input_minSize)){input_minSize = opt$input_minSize}else{input_minSize = 15}
+if(!is.null(opt$input_maxSize)){input_maxSize = opt$input_maxSize}else{input_maxSize = 2000}
+if(!is.null(opt$input_randomization) & opt$input_randomization != "NULL"){input_randomization = opt$input_randomization}else{input_randomization = NULL}
+input_core = parallel::detectCores()
+if(!is.null(opt$input_reglocation)){input_reglocation = opt$input_reglocation}else{input_reglocation = "tss"} #proxReg
+#chipenrich、hybridenrich
+if(!is.null(opt$input_num_peak_threshould)){input_num_peak_threshould = opt$input_num_peak_threshould}else{input_num_peak_threshould = 1}
+#================================================================
+#run codes
+#================================================================
+suppressPackageStartupMessages(library(chipenrich))
+## ---- chipenrich----------------------------------------
+if (input_method == "chipenrich"){
+  results = chipenrich(peaks = input_peaks, genome = input_genome, genesets = input_geneset,
+                       locusdef = input_locusdef, qc_plots = FALSE, out_name = input_output_name, 
+                       mappability = input_mappability,
+                       min_geneset_size = input_minSize,
+                       max_geneset_size = input_maxSize,
+                       randomization = input_randomization,
+                       num_peak_threshold = input_num_peak_threshould,
+                       n_cores = input_core)
+}
+
+
+## ----polyenrich----------------------------------------
+if (input_method == "polyenrich"){
+  results = polyenrich(peaks = input_peaks, genome = input_genome, genesets = input_geneset,
+                       method = 'polyenrich',
+                       locusdef = input_locusdef, qc_plots = FALSE, out_name = input_output_name, 
+                       mappability = input_mappability,
+                       min_geneset_size = input_minSize,
+                       max_geneset_size = input_maxSize,
+                       randomization = input_randomization,
+                       n_cores = input_core)
+}
+
+## ----hybridenrich----------------------------------------
+if (input_method == "hybridenrich"){
+  results = hybridenrich(peaks = input_peaks, genome = input_genome, genesets = input_geneset,
+                         locusdef = input_locusdef, qc_plots = FALSE, out_name = input_output_name, 
+                         mappability = input_mappability,
+                         min_geneset_size = input_minSize,
+                         max_geneset_size = input_maxSize,
+                         randomization = input_randomization,
+                         num_peak_threshold = input_num_peak_threshould,
+                         n_cores = input_core)
+}
+
+## ----proxReg----------------------------------------
+if (input_method == "proxReg"){
+  results = proxReg(peaks = input_peaks, reglocation = input_reglocation,
+                         genome = input_genome, genesets=input_geneset, 
+                         min_geneset_size = input_minSize,
+                         max_geneset_size = input_maxSize,
+                         randomization = input_randomization,
+                         out_name=input_output_name,
+                         n_cores = input_core)
+}
+
+## ----broadenrich----------------------------------------peaks_H3K4me3_GM12878---
+if (input_method == "broadenrich"){
+  results = broadenrich(peaks = input_peaks, genome = input_genome, genesets = input_geneset,
+                        locusdef = input_locusdef, qc_plots = FALSE, out_name = input_output_name, 
+                        mappability = input_mappability,
+                        min_geneset_size = input_minSize,
+                        max_geneset_size = input_maxSize,
+                        randomization = input_randomization,
+                        n_cores = input_core)
+}
+ 
+#===============================================================================
+# 输出
+#===============================================================================
+output_peaks = opt$output_peaks
+output_peaks_per_gene = opt$output_peaks_per_gene
+output_enrich_result = opt$output_enrich_results
+
+if (!is.null(output_peaks)){
+  write.csv(results$peaks, file = output_peaks)  
+}
+
+if (!is.null(output_peaks_per_gene)){
+  if (input_method != "proxReg"){
+    write.csv(results$peaks_per_gene, file = output_peaks_per_gene)  
+  }  
+}
+
+if (!is.null(output_enrich_result)){
+  write.csv(results$results, file = output_enrich_result)  
+}
+