Last updated: 2017-12-13

Code version: 3ed7074

The goal of this analysis is to create nice plots showing that we are getting as much information as the 1 lane from the Mayer sample. I will do this with our merged data vs. their 1 lane.

Genes from IGV that I want to use:

  • HERPUD1 chr16:56,964,002-56,979,793

  • ACTB chr7:5,564,779-5,572,232

  • CCNB2 chr15:59,396,707-59,401,006

  • chr11:234,336-239,997

  • KIAA0100 chr17:26,968,078-26,974,887

  • HECTD1 chr14:31,672,040-31,681,043

  • STAG1 chr3:136,469,421-136,472,771

Load Packages:

library(Gviz)
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs
The following objects are masked from 'package:base':

    anyDuplicated, append, as.data.frame, cbind, colMeans,
    colnames, colSums, do.call, duplicated, eval, evalq, Filter,
    Find, get, grep, grepl, intersect, is.unsorted, lapply,
    lengths, Map, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
    rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which, which.max, which.min

Attaching package: 'S4Vectors'
The following object is masked from 'package:base':

    expand.grid
Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: grid
library(GenomicRanges)
library(biomaRt)

Upload data:

chr= "chr7"
gen= "hg19"

options(ucscChromosomeNames=FALSE)
merged_data_7= DataTrack(range = "../data/merged_Net1.bam", genome = gen, type = "h", name = "Merged", window = -1, chromosome = "7")
mayer_data_7= DataTrack(range = "../data/SRR1575922-sort.bam", genome = gen, type = "h", name = "Mayer", window = -1, chromosome = "7")



data("geneModels")
grtrack= GeneRegionTrack(geneModels, genome = gen, chromosome = chr, name = "Gene Model")
itrack= IdeogramTrack(genome = gen, chromosome = chr)
gtrack = GenomeAxisTrack()

#plots
plotTracks(list(gtrack,merged_data_7, mayer_data_7), from = 5564779, to = 5572232,  background.title="darkblue",  background.panel = "#FFFEDB")

plotTracks(list(itrack, grtrack), transcriptAnnotation= "symbol", background.title="blue")

merged_anno_7= AnnotationTrack(range = "../data/merged_Net1.bam", genome = gen, name = "Merged", window = -1, chromosome = "7")
mayer_anno_7= AnnotationTrack(range = "../data/SRR1575922-sort.bam", genome = gen, name = "Mayer", window = -1, chromosome = "7")
plotTracks(list(merged_data_7, merged_anno_7), from = 5564779, to = 5572232)

plotTracks(list(mayer_data_7,mayer_anno_7), from = 5564779, to = 5572232)

Session information

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] biomaRt_2.34.0       Gviz_1.22.1          GenomicRanges_1.30.0
[4] GenomeInfoDb_1.14.0  IRanges_2.12.0       S4Vectors_0.16.0    
[7] BiocGenerics_0.24.0 

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.10.0           bitops_1.0-6                 
 [3] matrixStats_0.52.2            bit64_0.9-7                  
 [5] RColorBrewer_1.1-2            progress_1.1.2               
 [7] httr_1.3.1                    rprojroot_1.2                
 [9] tools_3.4.2                   backports_1.1.1              
[11] R6_2.2.2                      rpart_4.1-11                 
[13] Hmisc_4.0-3                   DBI_0.7                      
[15] lazyeval_0.2.1                colorspace_1.3-2             
[17] nnet_7.3-12                   gridExtra_2.3                
[19] prettyunits_1.0.2             RMySQL_0.10.13               
[21] bit_1.1-12                    curl_3.0                     
[23] compiler_3.4.2                git2r_0.19.0                 
[25] Biobase_2.38.0                htmlTable_1.11.0             
[27] DelayedArray_0.4.1            rtracklayer_1.38.2           
[29] scales_0.5.0                  checkmate_1.8.5              
[31] stringr_1.2.0                 digest_0.6.12                
[33] Rsamtools_1.30.0              foreign_0.8-69               
[35] rmarkdown_1.8                 XVector_0.18.0               
[37] base64enc_0.1-3               dichromat_2.0-0              
[39] pkgconfig_2.0.1               htmltools_0.3.6              
[41] ensembldb_2.2.0               BSgenome_1.46.0              
[43] htmlwidgets_0.9               rlang_0.1.4                  
[45] rstudioapi_0.7                RSQLite_2.0                  
[47] BiocInstaller_1.28.0          shiny_1.0.5                  
[49] bindr_0.1                     BiocParallel_1.12.0          
[51] acepack_1.4.1                 dplyr_0.7.4                  
[53] VariantAnnotation_1.24.2      RCurl_1.95-4.8               
[55] magrittr_1.5                  GenomeInfoDbData_0.99.1      
[57] Formula_1.2-2                 Matrix_1.2-12                
[59] Rcpp_0.12.14                  munsell_0.4.3                
[61] stringi_1.1.6                 yaml_2.1.15                  
[63] SummarizedExperiment_1.8.0    zlibbioc_1.24.0              
[65] plyr_1.8.4                    AnnotationHub_2.10.1         
[67] blob_1.1.0                    lattice_0.20-35              
[69] Biostrings_2.46.0             splines_3.4.2                
[71] GenomicFeatures_1.30.0        knitr_1.17                   
[73] XML_3.98-1.9                  glue_1.2.0                   
[75] evaluate_0.10.1               biovizBase_1.26.0            
[77] latticeExtra_0.6-28           data.table_1.10.4-3          
[79] httpuv_1.3.5                  gtable_0.2.0                 
[81] purrr_0.2.4                   tidyr_0.7.2                  
[83] assertthat_0.2.0              ggplot2_2.2.1                
[85] mime_0.5                      xtable_1.8-2                 
[87] AnnotationFilter_1.2.0        survival_2.41-3              
[89] tibble_1.3.4                  GenomicAlignments_1.14.1     
[91] AnnotationDbi_1.40.0          memoise_1.1.0                
[93] bindrcpp_0.2                  cluster_2.0.6                
[95] interactiveDisplayBase_1.16.0

This R Markdown site was created with workflowr