Last updated: 2020-03-08

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Processing gene scores (Corspan, Robospan and pRobospan)

probocov_gtex = get(load("/Users/kushaldey/Documents/Robocov-pages/data/Robocov_Precision_all_genes.rda"))
robocov_gtex = get(load("/Users/kushaldey/Documents/Robocov-pages/data/Robocov_Box_all_genes.rda"))
cor_gtex = get(load("/Users/kushaldey/Documents/Robocov-pages/data/Cor_pairwise_all_genes.rda"))

probospan = apply(probocov_gtex, 3, sum)/(53*53)
robospan = apply(robocov_gtex, 3, sum)/(53*53)
corspan = apply(cor_gtex, 3, sum)/(53*53)

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(probospan), ensembl_gene_symbol[,1]), 2]

probospan2 = probospan[which(!is.na(gene_symbols))] 
names(probospan2) = gene_symbols[which(!is.na(gene_symbols))]

robospan2 = robospan[which(!is.na(gene_symbols))] 
names(robospan2) = gene_symbols[which(!is.na(gene_symbols))]

corspan2 = corspan[which(!is.na(gene_symbols))] 
names(corspan2) = gene_symbols[which(!is.na(gene_symbols))]
length(robospan2)
[1] 13148
corspan_top10 = names(corspan2)[order(corspan2, decreasing = T)[1:1600]]
df = cbind.data.frame(corspan_top10, 1)
write.table(df, file = "/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Corspan_mean.txt",
            quote = F, col.names = F, row.names = F, sep = "\t")
robospan2_df = read.table("/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Robospan_mean.txt")
dim(robospan2_df)
[1] 1600    2
probospan2_df = read.table("/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/pRobospan_mean.txt")
dim(probospan2_df)
[1] 1600    2
corspan2_df = read.table("/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/Corspan_mean.txt")
dim(corspan2_df)
[1] 1600    2

Housekeeping genes

housekeep = read.table("/Users/kushaldey/Documents/Robocov-pages/data/housekeeping_genes.txt")
head(housekeep)
     V1        V2
1  AAAS NM_015665
2 AAGAB NM_024666
3  AAMP NM_001087
4  AAR2 NM_015511
5  AARS NM_001605
6 AARS2 NM_020745
gene_names_gtex = as.character(read.table("/Users/kushaldey/Documents/Robocov-pages/data/Gene_Scores/ensembl_and_hgnc_symbols.txt")[,2])
length(intersect(housekeep[,1], robospan2_df[,1]))/length(intersect(housekeep[,1], gene_names_gtex))/ (1600/13500)
[1] 0.8364218
length(intersect(housekeep[,1], probospan2_df[,1]))/length(intersect(housekeep[,1], gene_names_gtex))/ (1600/13500)
[1] 0.1440364
length(intersect(housekeep[,1], corspan2_df[,1]))/length(intersect(housekeep[,1], gene_names_gtex))/ (1600/13500)
[1] 0.7252358
seg_gtex = read.table("/Users/kushaldey/Documents/Mouse_Humans/data/Gene_Scores/Fin_GTEx_WholeBlood.txt")
dim(seg_gtex)
[1] 1983    2
length(intersect(seg_gtex[,1], robospan2_df[,1]))/length(intersect(seg_gtex[,1], gene_names_gtex))/ (1600/13500)
[1] 1.480824
length(intersect(seg_gtex[,1], probospan2_df[,1]))/length(intersect(seg_gtex[,1], gene_names_gtex))/ (1600/13500)
[1] 2.524858
length(intersect(seg_gtex[,1], corspan2_df[,1]))/length(intersect(seg_gtex[,1], gene_names_gtex))/ (1600/13500)
[1] 1.459517
head(seg_gtex, 50)
         V1 V2
1       FGR  1
2    CASP10  1
3  SLC22A16  1
4    SLC4A1  1
5     SKAP2  1
6   FAM214B  1
7       MPO  1
8     ITGAL  1
9    ITGA2B  1
10   KRT33A  1
11  ALDH3B1  1
12  LGALS14  1
13 CEACAM21  1
14  SLC13A2  1
15     MATK  1
16    CD79B  1
17     E2F2  1
18     NADK  1
19   TFAP2D  1
20  PGLYRP1  1
21    MMP25  1
22     IL32  1
23 TRAF3IP3  1
24      CD4  1
25    ABHD5  1
26    PLAUR  1
27   TYROBP  1
28      LTF  1
29    ALOX5  1
30 SLC25A39  1
31      CD6  1
32    TACC3  1
33     ACPP  1
34  CCDC88C  1
35      BID  1
36  SLC11A1  1
37    MARCO  1
38    RUNX3  1
39 SERPINB1  1
40   SLC7A9  1
41  SLC45A4  1
42    RNF10  1
43     DEF6  1
44     TYMP  1
45  RNASET2  1
46     CD44  1
47   SLAMF7  1
48   BTN3A1  1
49   IFNGR1  1
50   SH2D2A  1

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     

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_1.0.1        digest_0.6.19    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.4  
 [7] magrittr_1.5      git2r_0.23.0      evaluate_0.12    
[10] stringi_1.4.3     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.7.0     rmarkdown_1.10    tools_3.5.1      
[16] stringr_1.4.0     yaml_2.2.0        compiler_3.5.1   
[19] htmltools_0.3.6   knitr_1.20

This reproducible R Markdown analysis was created with workflowr 1.1.1