update

Author: junjunlab

NAMESPACE

@@ -16,6 +16,8 @@ export(enrichment_plot1)
 export(enrichment_plot2)
 export(export_genome_occupancy)
 export(feature_plot)
+export(find_strong_peaks)
+export(find_weak_peaks)
 export(frame_plot)
 export(gene_differential_analysis)
 export(generate_kmers)
@@ -71,6 +73,8 @@ exportMethods(enrichment_plot1)
 exportMethods(enrichment_plot2)
 exportMethods(export_genome_occupancy)
 exportMethods(feature_plot)
+exportMethods(find_strong_peaks)
+exportMethods(find_weak_peaks)
 exportMethods(frame_plot)
 exportMethods(gene_differential_analysis)
 exportMethods(generate_summary)
@@ -125,6 +129,7 @@ importFrom(Rsamtools,scanBam)
 importFrom(Rsamtools,scanBamFlag)
 importFrom(data.table,`:=`)
 importFrom(data.table,as.data.table)
+importFrom(data.table,rleid)
 importFrom(data.table,tstrsplit)
 importFrom(dplyr,"%>%")
 importFrom(dplyr,arrange)
@@ -142,8 +147,10 @@ importFrom(dplyr,rename)
 importFrom(dplyr,select)
 importFrom(dplyr,slice_max)
 importFrom(dplyr,summarise)
+importFrom(dplyr,ungroup)
 importFrom(fastplyr,f_arrange)
 importFrom(fastplyr,f_filter)
+importFrom(fastplyr,f_full_join)
 importFrom(fastplyr,f_group_by)
 importFrom(fastplyr,f_inner_join)
 importFrom(fastplyr,f_left_join)
@@ -178,6 +185,7 @@ importFrom(ggside,scale_xsidey_continuous)
 importFrom(magrittr,"%>%")
 importFrom(methods,new)
 importFrom(parallel,detectCores)
+importFrom(purrr,map)
 importFrom(purrr,map_df)
 importFrom(scales,label_log)
 importFrom(stats,density)

R/class.R

@@ -10,7 +10,8 @@ globalVariables(c(".", ".I", "enrich", "exonlen", "gene", "gene_name", "idnew","
                   "occurrence", "pause_score", "pep_seq", "ratio", "rel_pause", "tripep_val","motif","nt_pos",
                   "sample_group","sum_pi","counts.y", "periodicity.x","codons","log2FoldChange","Amplitude",
                   "Period","mapped", "pvalue", "seq_type","ccdf","pos3sp", "pos3st", "pos5sp", "pos5st",
-                  "sm1", "sm2", "smratio","bin", "nmft", "winstart","ci_high", "ci_low","norm.x","norm.y"))
+                  "sm1", "sm2", "smratio","bin", "nmft", "winstart","ci_high", "ci_low","norm.x","norm.y",
+                  "above", "background_mean", "group", "ip", "tt"))
 
 
 #' ribotrans Class