#knitr::opts_chunk$set(echo = TRUE) library(dplyr) library(ggplot2) library(PMCMRplus) library(data.table) library(ggsignif) #melt_data_localization <- "/home/smaegol/storage/analyses/tail_seq_5/ALL/processing_out/all_samples_2_3_4_5_anal.tsv" #data_melt<-fread(melt_data_localization)
#data_processed <- process_data(data_melt)
reporterl1_urid <- analyze_uridylation(data_processed,"REPORTERL1_overexp","OVR",include_jitter=T,facet_projects = TRUE,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10")) print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot)
ovr_mapping_pos <- plot_mapping_positions(data_processed,'REPORTERL1_overexp','OVR',conditions = c("CNTRL"),mapping_position_min = 8900, mapping_position_max = 9200, facet_projects = T)
reporterl1_urid <- analyze_uridylation(data_processed,"REPORTERL1_overexp","OVR",include_jitter=T,facet_projects = TRUE,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10"),mapping_position_max = 9010) print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot) print("All sqeuencing run together:") reporterl1_urid <- analyze_uridylation(data_processed,"REPORTERL1_overexp","OVR",include_jitter=T,facet_projects = FALSE,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10"),mapping_position_max = 9010) print("Dunn test statistics:") print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot) #analyze_uridylation()
print("Tailseq_2 and Tailseq_4 only:") reporterl1_urid <- analyze_uridylation(data_processed,"REPORTERL1_overexp","OVR",include_jitter=T,facet_projects = FALSE,project = c("Tailseq_4","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10"),mapping_position_max = 9010) print("Dunn test statistics:") print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot) #analyze_uridylation()
``` {r tail lengths distribution,message=FALSE,warning=FALSE,echo=FALSE} distrib<-plot_tail_length_distribution(data_processed,"LEAP_AU","LEAP",conditions=c("19A","19A3U"),max_tail_length = 30, min_tail_length=10,facet_conditions = T,AUtail = 'Ataila') print(distrib)
# Reporter KD #### Analyzed first for all mapped reads, irrespective of mapping position (UTR,SV40 signal), only for TUTases and MOV10: ```r reporterl1_kd <- analyze_uridylation(processed_data2,"REPORTERL1KD","KD",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot) reporterl1_kd <- analyze_uridylation(processed_data2,"REPORTERL1KD","KD",include_jitter=T,facet_projects = TRUE,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot)
kd_mapping_pos <- plot_mapping_positions(processed_data2,'REPORTERL1KD','KD',conditions = c("CNTRLKD"),mapping_position_min = 8000, mapping_position_max = 9200, facet_projects = T) print(kd_mapping_pos)
After filtering To BGH site:
reporterl1_kd <- analyze_uridylation(processed_data2,"REPORTERL1KD","KD",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD"),mapping_position_min = 8600,mapping_position_max = 8700) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot)
After filtering to before BGH site:
reporterl1_kd <- analyze_uridylation(processed_data2,"REPORTERL1KD","KD",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD"),mapping_position_max = 8600) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot)
After filtering to HGC only:
processed_data_no_MGC <- processed_data2 %>% filter((condition=="CNTRLKD" & replicate<7) | condition!="CNTRLKD") reporterl1_kd <- analyze_uridylation(processed_data_no_MGC,"REPORTERL1KD","KD",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot) reporterl1_kd <- analyze_uridylation(processed_data_no_MGC,"REPORTERL1KD","KD",include_jitter=T,facet_projects = T,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot)
After filtering to MGC only:
processed_data_no_MGC <- processed_data2 %>% filter((condition=="CNTRLKD" & replicate %in% c(1,2,3,7,8,9)) | condition!="CNTRLKD") reporterl1_kd <- analyze_uridylation(processed_data_no_MGC,"REPORTERL1KD","KD",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot) reporterl1_kd <- analyze_uridylation(processed_data_no_MGC,"REPORTERL1KD","KD",include_jitter=T,facet_projects = T,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRLKD","TUT7KD","TUT4KD","MOV10KD","TUT4TUT7KD","TUT4TUT7MOV10KD")) print(reporterl1_kd$dunn_test) print(reporterl1_kd$plot)
reporterl1_urid <- analyze_uridylation(data_processed,"GAPDH","OVR",include_jitter=T,facet_projects = F,project = c("Tailseq_4","Tailseq_5","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10")) print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot) reporterl1_urid <- analyze_uridylation(data_processed,"GAPDH","OVR",include_jitter=T,facet_projects = T,project = c("Tailseq_4","Tailseq_5","Tailseq_3","Tailseq_2"),conditions=c("CNTRL","TUT7WT","TUT7MT","TUT4WT","TUT4MT","MOV10")) print(reporterl1_urid$dunn_test) print(reporterl1_urid$plot)
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