Last updated: 2020-03-08

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library(Robocov)
library(corrplot)
corrplot 0.84 loaded
library(ggplot2)
Warning: package 'ggplot2' was built under R version 3.5.2

Here we illustrare the Robocov estimates for a few genes of interest and then introduce the concept of Robospan.

robocov_gtex = get(load("/Users/kushaldey/Documents/Robocov-pages/data/Robocov_Box_all_genes.rda"))
dim(robocov_gtex)
[1]    53    53 16069

HBB (ENSG00000244734)

corrplot(robocov_gtex[,,"ENSG00000244734"],  diag = TRUE,
         col = colorRampPalette(c("blue", "white", "red"))(200),
         tl.pos = "td", tl.cex = 0.4, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "upper")

robospan = apply(robocov_gtex, 3, sum)/(53*53)
plot(density(robospan), xlab = "Robospan score", ylab = "density")

robospan[order(robospan, decreasing = T)[1:10]]
ENSG00000134184 ENSG00000226278 ENSG00000184674 ENSG00000163682 
      0.7032426       0.6950521       0.6912778       0.6872412 
ENSG00000233927 ENSG00000260246 ENSG00000204792 ENSG00000183298 
      0.6794906       0.6776832       0.6722359       0.6624388 
ENSG00000196436 ENSG00000271581 
      0.6610709       0.6344899 
robospan["ENSG00000244734"]
ENSG00000244734 
      0.1639102 
corrplot(robocov_gtex[,,"ENSG00000019991"],  diag = TRUE,
         col = colorRampPalette(c("blue", "white", "red"))(200),
         tl.pos = "td", tl.cex = 0.4, tl.col = "black",
         rect.col = "white",na.label.col = "white",
         method = "color", type = "upper")

Ensembl and Gene symbol names

ensembl_gene_symbol = read.table("/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/ensembl_and_hgnc_symbols.txt")
head(ensembl_gene_symbol)
               V1       V2
1 ENSG00000000419     DPM1
2 ENSG00000000457    SCYL3
3 ENSG00000000460 C1orf112
4 ENSG00000000938      FGR
5 ENSG00000000971      CFH
6 ENSG00000001036    FUCA2
gene_symbols = ensembl_gene_symbol[match(names(robospan), ensembl_gene_symbol[,1]), 2]
robospan2 = robospan[which(!is.na(gene_symbols))] 
names(robospan2) = gene_symbols[which(!is.na(gene_symbols))]

Robospan mean

genes = names(robospan2)[order(robospan2, decreasing = T)[1:1600]]
df = cbind.data.frame(genes, 1)
write.table(df, file = "/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Robospan_mean.txt",
            row.names = F, col.names = F, sep = "\t", quote=F)

Robospan Num Up 0.1

robospan = apply(robocov_gtex, 3, function(x) length(which(x > 0.1)))/(53*53)
gene_symbols = ensembl_gene_symbol[match(names(robospan), ensembl_gene_symbol[,1]), 2]
robospan2 = robospan[which(!is.na(gene_symbols))] 
names(robospan2) = gene_symbols[which(!is.na(gene_symbols))]
genes = names(robospan2)[order(robospan2, decreasing = T)[1:1600]]
df = cbind.data.frame(genes, 1)
write.table(df, file = "/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Robospan_Numbin_up_0_1.txt",
            row.names = F, col.names = F, sep = "\t", quote=F)

Robospan mean Blood

robospan = apply(robocov_gtex[,53,], 2, mean)
gene_symbols = ensembl_gene_symbol[match(names(robospan), ensembl_gene_symbol[,1]), 2]
robospan2 = robospan[which(!is.na(gene_symbols))] 
names(robospan2) = gene_symbols[which(!is.na(gene_symbols))]
genes = names(robospan2)[order(robospan2, decreasing = T)[1:1600]]
df = cbind.data.frame(genes, 1)
write.table(df, file = "/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Robospan_Mean_Blood.txt",
            row.names = F, col.names = F, sep = "\t", quote=F)

Session information

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/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] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] ggplot2_3.1.1 corrplot_0.84 Robocov_0.1-6

loaded via a namespace (and not attached):
 [1] gmp_0.5-13.2      Rcpp_1.0.1        pillar_1.3.1     
 [4] compiler_3.5.1    git2r_0.23.0      CVXR_0.99-2      
 [7] plyr_1.8.4        workflowr_1.1.1   R.methodsS3_1.7.1
[10] R.utils_2.7.0     tools_3.5.1       digest_0.6.19    
[13] bit_1.1-14        tibble_2.1.1      evaluate_0.12    
[16] gtable_0.3.0      lattice_0.20-35   pkgconfig_2.0.2  
[19] rlang_0.4.2       Matrix_1.2-14     yaml_2.2.0       
[22] withr_2.1.2       dplyr_0.8.0.1     Rmpfr_0.7-1      
[25] ECOSolveR_0.4     stringr_1.4.0     knitr_1.20       
[28] tidyselect_0.2.5  rprojroot_1.3-2   bit64_0.9-7      
[31] grid_3.5.1        glue_1.3.1        R6_2.4.0         
[34] rmarkdown_1.10    purrr_0.3.2       magrittr_1.5     
[37] whisker_0.3-2     backports_1.1.4   scales_1.0.0     
[40] htmltools_0.3.6   scs_1.1-1         assertthat_0.2.1 
[43] colorspace_1.4-1  stringi_1.4.3     lazyeval_0.2.2   
[46] munsell_0.5.0     crayon_1.3.4      R.oo_1.22.0

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