Last updated: 2020-08-26

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Knit directory: T1D_epitranscriptome/

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Rmd 0d46101 scottzijiezhang 2020-08-26 wflow_publish(“analysis/coveragePlot.Rmd”)

Coverage plot for stimulated human islets

library(RADAR)
load("~/Rohit_T1D/stim_Patient_islets/stim_patient_RADAR.RData")
stim_patient_RADAR <- PrepCoveragePlot(stim_patient_RADAR)
library(ggsci)
plotGeneCov(stim_patient_RADAR, geneName = "ADAR", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ADAR")

plotGeneCov(stim_patient_RADAR, geneName = "ADAR", libraryType = "opposite", ZoomIn = c(154607900, 154608224),adjustExprLevel = TRUE, center = "mean")+ggtitle("ADAR zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "CD14", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("CD14")

plotGeneCov(stim_patient_RADAR, geneName = "CD14", libraryType = "opposite", ZoomIn = c(140633131,  140633428),adjustExprLevel = TRUE, center = "mean")+ggtitle("CD14 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "CLU", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("CLU")

plotGeneCov(stim_patient_RADAR, geneName = "CLU", libraryType = "opposite", ZoomIn = c(27611562, 27611811),adjustExprLevel = TRUE, center = "mean")+ggtitle("CLU zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "CTSS", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("CTSS")

plotGeneCov(stim_patient_RADAR, geneName = "CTSS", libraryType = "opposite", ZoomIn = c(150730393,  150730642),adjustExprLevel = TRUE, center = "mean")+ggtitle("CTSS zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "DHX58", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("DHX58")

plotGeneCov(stim_patient_RADAR, geneName = "DHX58", libraryType = "opposite", ZoomIn = c(42101355,  42101604),adjustExprLevel = TRUE, center = "mean")+ggtitle("DHX58 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "EP300", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("EP300")

plotGeneCov(stim_patient_RADAR, geneName = "EP300", libraryType = "opposite", ZoomIn = c(41176692,  41177041),adjustExprLevel = TRUE, center = "mean")+ggtitle("EP300 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "GBP1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("GBP1")

plotGeneCov(stim_patient_RADAR, geneName = "GBP1", libraryType = "opposite", ZoomIn = c(89062955,   89063304),adjustExprLevel = TRUE, center = "mean")+ggtitle("GBP1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "HIST1H2BD", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("HIST1H2BD")

plotGeneCov(stim_patient_RADAR, geneName = "HIST1H2BD", libraryType = "opposite", ZoomIn = c(26170862, 26171262),adjustExprLevel = TRUE, center = "mean")+ggtitle("HIST1H2BD zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "HIST2H2BE", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("HIST2H2BE")

plotGeneCov(stim_patient_RADAR, geneName = "HIST2H2BE", libraryType = "opposite", ZoomIn = c(149886038, 149886287),adjustExprLevel = TRUE, center = "mean")+ggtitle("HIST2H2BE zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "IFI6", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("IFI6")

plotGeneCov(stim_patient_RADAR, geneName = "IFI6", libraryType = "opposite", ZoomIn = c(27672064,   27672313),adjustExprLevel = TRUE, center = "mean")+ggtitle("IFI6 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "IFIT2", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("IFIT2")

plotGeneCov(stim_patient_RADAR, geneName = "IFIT2", libraryType = "opposite", ZoomIn = c(89301799,  89302248),adjustExprLevel = TRUE, center = "mean")+ggtitle("IFIT2 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "IFIT5", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("IFIT5")

plotGeneCov(stim_patient_RADAR, geneName = "ISG20", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ISG20")

plotGeneCov(stim_patient_RADAR, geneName = "ISG20", libraryType = "opposite", ZoomIn = c(88638702,  88639200),adjustExprLevel = TRUE, center = "mean")+ggtitle("ISG20 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "JAK2", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("JAK2")

plotGeneCov(stim_patient_RADAR, geneName = "JAK2", libraryType = "opposite", ZoomIn = c(4985145,    4985594),adjustExprLevel = TRUE, center = "mean")+ggtitle("JAK2 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "MX1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("MX1")

plotGeneCov(stim_patient_RADAR, geneName = "MX1", libraryType = "opposite", ZoomIn = c(41427039,    41427488),adjustExprLevel = TRUE, center = "mean")+ggtitle("MX1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "NMI", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("NMI")

plotGeneCov(stim_patient_RADAR, geneName = "NMI", libraryType = "opposite", ZoomIn = c(151282784,   151283033),adjustExprLevel = TRUE, center = "mean")+ggtitle("NMI zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "NR1D1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("NR1D1")

plotGeneCov(stim_patient_RADAR, geneName = "NR1D1", libraryType = "opposite", ZoomIn = c(40100526,  40100775),adjustExprLevel = TRUE, center = "mean")+ggtitle("NR1D1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "OAS3", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("OAS3")

plotGeneCov(stim_patient_RADAR, geneName = "OAS3", libraryType = "opposite", ZoomIn = c(112938233,  112938682),adjustExprLevel = TRUE, center = "mean")+ggtitle("OAS3 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "OASL", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean", split = T)+ggtitle("OASL")

plotGeneCov(stim_patient_RADAR, geneName = "OASL", libraryType = "opposite", ZoomIn = c(121020342,  121020440),adjustExprLevel = TRUE, center = "mean")+ggtitle("OASL zoom in")

I think the data for this gene has something wrong. The coverage of IP looks like PCR duplicates…

plotGeneCov(stim_patient_RADAR, geneName = "PARP14", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("PARP14")

plotGeneCov(stim_patient_RADAR, geneName = "PARP14", libraryType = "opposite", ZoomIn = c(122680725,122681174),adjustExprLevel = TRUE, center = "mean")+ggtitle("PARP14 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "PIK3AP1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("PIK3AP1")

plotGeneCov(stim_patient_RADAR, geneName = "PIK3AP1", libraryType = "opposite", ZoomIn = c(96709726,    96710175),adjustExprLevel = TRUE, center = "mean")+ggtitle("PIK3AP1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "PLSCR1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("PLSCR1")

plotGeneCov(stim_patient_RADAR, geneName = "PLSCR1", libraryType = "opposite", ZoomIn = c(146544396,    146544794),adjustExprLevel = TRUE, center = "mean")+ggtitle("PLSCR1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "PML", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("PML")

plotGeneCov(stim_patient_RADAR, geneName = "PML", libraryType = "opposite", ZoomIn = c(73994623,    73994972),adjustExprLevel = TRUE, center = "mean")+ggtitle("PML zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "RSAD2", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("RSAD2")

plotGeneCov(stim_patient_RADAR, geneName = "RSAD2", libraryType = "opposite", ZoomIn = c(6896154,   6896403),adjustExprLevel = TRUE, center = "mean")+ggtitle("RSAD2 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "SP100", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("SP100")

plotGeneCov(stim_patient_RADAR, geneName = "SP100", libraryType = "opposite", ZoomIn = c(230416633, 230417791),adjustExprLevel = TRUE, center = "mean")+ggtitle("SP100 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "SSC5D", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("SSC5D")

plotGeneCov(stim_patient_RADAR, geneName = "SSC5D", libraryType = "opposite", ZoomIn = c(55500585,  55500834),adjustExprLevel = TRUE, center = "mean")+ggtitle("SSC5D in")

plotGeneCov(stim_patient_RADAR, geneName = "TLR3", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("TLR3")

plotGeneCov(stim_patient_RADAR, geneName = "TLR3", libraryType = "opposite", ZoomIn = c(186076618, 186077067),adjustExprLevel = TRUE, center = "mean")+ggtitle("TLR3 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "TNFAIP3", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("TNFAIP3")

plotGeneCov(stim_patient_RADAR, geneName = "TNFAIP3", libraryType = "opposite", ZoomIn = c(137867188,   137867587),adjustExprLevel = TRUE, center = "mean")+ggtitle("TNFAIP3 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "TREX1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("TREX1")

plotGeneCov(stim_patient_RADAR, geneName = "TRIM56", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("TRIM56")

plotGeneCov(stim_patient_RADAR, geneName = "TRIM56", libraryType = "opposite", ZoomIn = c(101085389,    101085638   ),adjustExprLevel = TRUE, center = "mean")+ggtitle("TRIM56 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "USP18", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("USP18")

plotGeneCov(stim_patient_RADAR, geneName = "USP18", libraryType = "opposite", ZoomIn = c(18149890,  18150189),adjustExprLevel = TRUE, center = "mean")+ggtitle("USP18 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "XAF1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("XAF1")

plotGeneCov(stim_patient_RADAR, geneName = "XAF1", libraryType = "opposite", ZoomIn = c(6774453,    6774902 ),adjustExprLevel = TRUE, center = "mean")+ggtitle("XAF1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "ZBTB1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ZBTB1")

plotGeneCov(stim_patient_RADAR, geneName = "ZBTB1", libraryType = "opposite", ZoomIn = c(64522044,  64523000    ),adjustExprLevel = TRUE, center = "mean")+ggtitle("ZBTB1 zoom in")

plotGeneCov(stim_patient_RADAR, geneName = "ZC3HAV1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ZC3HAV1")

plotGeneCov(stim_patient_RADAR, geneName = "ZC3HAV1", libraryType = "opposite", ZoomIn = c(139060680,   139061179       ),adjustExprLevel = TRUE, center = "mean")+ggtitle("ZC3HAV1 zoom in")

Coverage plot for T1D islets

load("~/Rohit_T1D/stim_Patient_islets/T1D_patient_RADAR.RData")
T1D_patient_RADAR <- PrepCoveragePlot (T1D_patient_RADAR)
plotGeneCov(T1D_patient_RADAR, geneName = "EP300", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("EP300")

plotGeneCov(T1D_patient_RADAR, geneName = "EP300", libraryType = "opposite", ZoomIn = c(41092759,   41093008),adjustExprLevel = TRUE, center = "mean")+ggtitle("EP300 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "IFIT2", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("IFIT2")

plotGeneCov(T1D_patient_RADAR, geneName = "IFIT2", libraryType = "opposite", ZoomIn = c(89307979,   89308228),adjustExprLevel = TRUE, center = "mean")+ggtitle("IFIT2 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "JAK2", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("JAK2")

plotGeneCov(T1D_patient_RADAR, geneName = "JAK2", libraryType = "opposite", ZoomIn = c(5055585, 5055834 ),adjustExprLevel = TRUE, center = "mean")+ggtitle("JAK2 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "NMI", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("NMI")

plotGeneCov(T1D_patient_RADAR, geneName = "NMI", libraryType = "opposite", ZoomIn = c(149579860,    149580811   ),adjustExprLevel = TRUE, center = "mean")+ggtitle("NMI zoom in")

This is a false discovery due to very low coverage.

plotGeneCov(T1D_patient_RADAR, geneName = "PARP14", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("PARP14")

plotGeneCov(T1D_patient_RADAR, geneName = "PARP14", libraryType = "opposite", ZoomIn = c(122727684, 122728033   ),adjustExprLevel = TRUE, center = "mean")+ggtitle("PARP14 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "TLR3", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("TLR3")

plotGeneCov(T1D_patient_RADAR, geneName = "TLR3", libraryType = "opposite", ZoomIn = c(186082782,   186083031   ),adjustExprLevel = TRUE, center = "mean")+ggtitle("TLR3 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "ZBTB1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ZBTB1")

plotGeneCov(T1D_patient_RADAR, geneName = "ZBTB1", libraryType = "opposite", ZoomIn = c(64522044,   64522944    ),adjustExprLevel = TRUE, center = "mean")+ggtitle("ZBTB1 zoom in")

plotGeneCov(T1D_patient_RADAR, geneName = "ZC3HAV1", libraryType = "opposite", adjustExprLevel = TRUE, center = "mean")+ggtitle("ZC3HAV1")

plotGeneCov(T1D_patient_RADAR, geneName = "ZC3HAV1", libraryType = "opposite", ZoomIn = c(139108922,    139109371   ),adjustExprLevel = TRUE, center = "mean")+ggtitle("ZC3HAV1 zoom in")


sessionInfo()
R version 3.5.3 (2019-03-11)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 17.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ggsci_2.9                 RADAR_0.2.3              
 [3] qvalue_2.14.1             RcppArmadillo_0.9.400.2.0
 [5] Rcpp_1.0.1                RColorBrewer_1.1-2       
 [7] gplots_3.0.1.1            doParallel_1.0.14        
 [9] iterators_1.0.10          foreach_1.4.4            
[11] ggplot2_3.1.1             Rsamtools_1.34.1         
[13] Biostrings_2.50.2         XVector_0.22.0           
[15] GenomicFeatures_1.34.8    AnnotationDbi_1.44.0     
[17] Biobase_2.42.0            GenomicRanges_1.34.0     
[19] GenomeInfoDb_1.18.2       IRanges_2.16.0           
[21] S4Vectors_0.20.1          BiocGenerics_0.28.0      

loaded via a namespace (and not attached):
 [1] bitops_1.0-6                matrixStats_0.54.0         
 [3] fs_1.3.0                    bit64_0.9-7                
 [5] progress_1.2.0              httr_1.4.0                 
 [7] rprojroot_1.3-2             tools_3.5.3                
 [9] backports_1.1.4             R6_2.4.0                   
[11] rpart_4.1-13                KernSmooth_2.23-15         
[13] Hmisc_4.2-0                 DBI_1.0.0                  
[15] lazyeval_0.2.2              colorspace_1.4-1           
[17] nnet_7.3-12                 withr_2.1.2                
[19] gridExtra_2.3               tidyselect_0.2.5           
[21] prettyunits_1.0.2           DESeq2_1.22.2              
[23] bit_1.1-14                  compiler_3.5.3             
[25] git2r_0.25.2                htmlTable_1.13.1           
[27] DelayedArray_0.8.0          labeling_0.3               
[29] rtracklayer_1.42.2          checkmate_1.9.1            
[31] caTools_1.17.1.2            scales_1.0.0               
[33] genefilter_1.64.0           stringr_1.4.0              
[35] digest_0.6.18               foreign_0.8-71             
[37] rmarkdown_1.12              base64enc_0.1-3            
[39] pkgconfig_2.0.2             htmltools_0.3.6            
[41] htmlwidgets_1.3             rlang_0.4.0                
[43] rstudioapi_0.10             RSQLite_2.1.1              
[45] BiocParallel_1.16.6         gtools_3.8.1               
[47] acepack_1.4.1               dplyr_0.8.0.1              
[49] RCurl_1.95-4.12             magrittr_1.5               
[51] GenomeInfoDbData_1.2.0      Formula_1.2-3              
[53] Matrix_1.2-17               munsell_0.5.0              
[55] stringi_1.4.3               whisker_0.3-2              
[57] yaml_2.2.0                  SummarizedExperiment_1.12.0
[59] zlibbioc_1.28.0             plyr_1.8.4                 
[61] grid_3.5.3                  blob_1.1.1                 
[63] gdata_2.18.0                crayon_1.3.4               
[65] lattice_0.20-38             splines_3.5.3              
[67] annotate_1.60.1             hms_0.4.2                  
[69] locfit_1.5-9.1              knitr_1.22                 
[71] pillar_1.3.1                geneplotter_1.60.0         
[73] reshape2_1.4.3              codetools_0.2-16           
[75] biomaRt_2.38.0              XML_3.98-1.19              
[77] glue_1.3.1                  evaluate_0.13              
[79] latticeExtra_0.6-28         data.table_1.12.2          
[81] gtable_0.3.0                purrr_0.3.2                
[83] assertthat_0.2.1            xfun_0.6                   
[85] xtable_1.8-4                survival_2.44-1.1          
[87] tibble_2.1.1                GenomicAlignments_1.18.1   
[89] memoise_1.1.0               cluster_2.0.7-1            
[91] workflowr_1.3.0