Last updated: 2017-11-09

Code version: aee8225

I will look at genome feature overlap with the Netseq1 libary. I will start with one sample then move to more once the code is working. I will look specifically at overlap with CTCF sites.

Load libraries:

library(genomation)
Loading required package: grid
library(genomationData)

Load gata:

CTCF_gen= readGeneric(file = "../data/hg19.GM72.CTCF", header=FALSE, keep.all.metadata = TRUE)
#bed file for one of my libraries  
# to get from midway
#scp brimittleman@midway2.rcc.uchicago.edu:/project2/gilad/briana/Net-seq/Net-seq1/data/cov/YG-SP-NET1-18486-dep-2017-10-13_S4_R1_001-sort.dedup.cov.bed .

cov.18486.dep= readGeneric(file= "../data/YG-SP-NET1-18486-dep-2017-10-13_S4_R1_001-sort.dedup.cov.bed", header = FALSE, keep.all.metadata = TRUE)

Data extaction:

Try to get the density of net-seq reads around CTCF sites

#sm=ScoreMatrixBin(target = cov.18486.dep, windows = CTCF_gen, bin.num = 10 )
#peak.annot = annotateWithFeature(CTCF_gen, cov.18486.dep, intersect.chr = TRUE)

Maybe the problem is the names of the coloumns.

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      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] genomationData_1.10.0 genomation_1.10.0    

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.13               plyr_1.8.4                
 [3] compiler_3.4.2             git2r_0.19.0              
 [5] GenomeInfoDb_1.14.0        XVector_0.18.0            
 [7] bitops_1.0-6               tools_3.4.2               
 [9] zlibbioc_1.24.0            digest_0.6.12             
[11] gridBase_0.4-7             tibble_1.3.4              
[13] gtable_0.2.0               evaluate_0.10.1           
[15] BSgenome_1.46.0            lattice_0.20-35           
[17] rlang_0.1.4                Matrix_1.2-11             
[19] DelayedArray_0.4.1         yaml_2.1.14               
[21] parallel_3.4.2             GenomeInfoDbData_0.99.1   
[23] rtracklayer_1.38.0         stringr_1.2.0             
[25] knitr_1.17                 hms_0.3                   
[27] Biostrings_2.46.0          S4Vectors_0.16.0          
[29] IRanges_2.12.0             stats4_3.4.2              
[31] rprojroot_1.2              data.table_1.10.4-3       
[33] impute_1.52.0              Biobase_2.38.0            
[35] R6_2.2.2                   plotrix_3.6-6             
[37] XML_3.98-1.9               BiocParallel_1.12.0       
[39] seqPattern_1.10.0          rmarkdown_1.6             
[41] reshape2_1.4.2             readr_1.1.1               
[43] ggplot2_2.2.1              magrittr_1.5              
[45] scales_0.5.0               backports_1.1.1           
[47] Rsamtools_1.30.0           htmltools_0.3.6           
[49] matrixStats_0.52.2         BiocGenerics_0.24.0       
[51] GenomicRanges_1.30.0       GenomicAlignments_1.14.0  
[53] SummarizedExperiment_1.8.0 colorspace_1.3-2          
[55] KernSmooth_2.23-15         stringi_1.1.5             
[57] lazyeval_0.2.1             munsell_0.4.3             
[59] RCurl_1.95-4.8

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