Last updated: 2019-05-21

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    Untracked:  bias.brca.csv
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    Untracked:  data/All_Data_V2.csv
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    Modified:   analysis/ALKATI_Filter_Cutoff_Analysis.Rmd
    Modified:   analysis/ALK_ExonImbalance_SKCM_Analysis.Rmd
    Modified:   analysis/TCGA_luad_data_parser.Rmd
    Modified:   analysis/alkati_cell_line_tae684_response.Rmd
    Modified:   analysis/alkati_subsampling_simulations.Rmd
    Modified:   analysis/baf3_alkati_transformations.Rmd
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Rmd f8e2d5e haiderinam 2019-02-17 Published Analysis on ALK expression levels #2

library(knitr)
library(tictoc)
library(workflowr)
This is workflowr version 1.3.0
Run ?workflowr for help getting started
library(VennDiagram)
Loading required package: grid
Loading required package: futile.logger
library(dplyr)

Attaching package: 'dplyr'
The following objects are masked from 'package:stats':

    filter, lag
The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union
library(foreach)
library(doParallel)
Loading required package: iterators
Loading required package: parallel
library(ggplot2)
library(reshape2)
library(RColorBrewer)
library(devtools)
library(ggsignif)
source("code/contab_maker.R")
source("code/alldata_compiler.R")
source("code/quadratic_solver.R")
source("code/mut_excl_genes_generator.R")
source("code/mut_excl_genes_datapoints.R")
source("code/simresults_generator.R")

######################Cleanup for GGPlot2#########################################
cleanup=theme_bw() +
  theme(plot.title = element_text(hjust=.5),
        panel.grid.major = element_blank(),
        panel.grid.major.y = element_blank(),
        panel.background = element_blank(),
        axis.line = element_line(color = "black"))

Making ALK Expression the plots:

alkati_merged_data=read.csv("output/all_data_skcm.csv")
alkati_merged_data$alkati=0
alkati_merged_data$alkati[alkati_merged_data$Ratio>=10&alkati_merged_data$mRNA_count>=500&alkati_merged_data$RSEM_normalized>=100]=1
alkati_merged_data$alkati=factor(alkati_merged_data$alkati,levels=c("1","0"))

  ggplot(alkati_merged_data,aes(x=mean_RPKM_1.19, y=mean_RPKM_20.29,color=factor(alkati)))+
    geom_abline(size=1)+
    geom_point(size=4)+
    ####Had to add this line to not overplot the alkati datapoint- Haider 1/31/19
    geom_point(data=alkati_merged_data[alkati_merged_data$alkati==1,],aes(x=mean_RPKM_1.19, y=mean_RPKM_20.29,color=factor(alkati)),size=4)+
    scale_x_continuous(trans = "log10",name="Exon 1:19 RPKM",breaks=c(1e-2,1e0,1e2),labels = parse(text = c("10^-2","10^0","10^2")),limits = c(1e-3,1e3))+
    scale_y_continuous(trans = "log10",name="Exon 20:29 RPKM",breaks=c(1e-2,1e0,1e2),labels = parse(text = c("10^-2","10^0","10^2")),limits = c(1e-3,1e3))+
    scale_color_brewer(palette="Set1",name="ALKATI",labels=c("Yes", "No"))+
    cleanup+
    theme(plot.title = element_text(hjust=.5),
          text = element_text(size=11,face = "bold"),
          axis.title = element_text(face="bold",size="11"),
          axis.text=element_text(face="bold",size="11",colour = "black"))+
    theme(legend.key.size = unit(30,"pt"))
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Removed 2 rows containing missing values (geom_point).

Version Author Date
dfdb600 haiderinam 2019-02-17
# ggsave("output/alkati_skcm_exonimbalance.pdf",width =12 ,height =10 ,units = "in",useDingbats=F)

Statistical test to see if ALK kinase domain expression was significantly higher than other domains

#Testing if both kinase and ALK expression are different
ks.test(alkati_merged_data$mean_RPKM_1.19,alkati_merged_data$mean_RPKM_20.29)
Warning in ks.test(alkati_merged_data$mean_RPKM_1.19,
alkati_merged_data$mean_RPKM_20.29): p-value will be approximate in the
presence of ties

    Two-sample Kolmogorov-Smirnov test

data:  alkati_merged_data$mean_RPKM_1.19 and alkati_merged_data$mean_RPKM_20.29
D = 0.40456, p-value < 2.2e-16
alternative hypothesis: two-sided
###We observed a significant difference between the distribution for the 20-29 exons and the 1-19 exons The reported p-value was 2-16.
###The p-value from a Chi-sq test was 2.2e-16 too
    #for all ALK data, not ALKATI
ov_expr_obs=c(sum(as.numeric(alkati_merged_data$Ratio20.29>1),na.rm = T),
              dim(alkati_merged_data)[1]-sum(as.numeric(alkati_merged_data$Ratio20.29>1),na.rm = T))
ov_expr_expected=c(round(dim(alkati_merged_data)[1]/2),
                   round(dim(alkati_merged_data)[1]/2))
overexpression=data.frame(rbind(ov_expr_obs,ov_expr_expected))
# overexpression=data.frame(rbind(c(338,13),c(176,176)))
colnames(overexpression)=c("Yes","No")
chisq.test(overexpression)

    Pearson's Chi-squared test with Yates' continuity correction

data:  overexpression
X-squared = 189.29, df = 1, p-value < 2.2e-16

sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.5

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] parallel  grid      stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] ggsignif_0.5.0      usethis_1.5.0       devtools_2.0.2     
 [4] RColorBrewer_1.1-2  reshape2_1.4.3      ggplot2_3.1.1      
 [7] doParallel_1.0.14   iterators_1.0.10    foreach_1.4.4      
[10] dplyr_0.8.1         VennDiagram_1.6.20  futile.logger_1.4.3
[13] workflowr_1.3.0     tictoc_1.0          knitr_1.23         

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5     xfun_0.7             remotes_2.0.4       
 [4] purrr_0.3.2          colorspace_1.4-1     htmltools_0.3.6     
 [7] yaml_2.2.0           rlang_0.3.4          pkgbuild_1.0.3      
[10] pillar_1.4.0         glue_1.3.1           withr_2.1.2         
[13] lambda.r_1.2.3       sessioninfo_1.1.1    plyr_1.8.4          
[16] stringr_1.4.0        munsell_0.5.0        gtable_0.3.0        
[19] codetools_0.2-16     evaluate_0.13        memoise_1.1.0       
[22] callr_3.2.0          ps_1.3.0             Rcpp_1.0.1          
[25] scales_1.0.0         backports_1.1.4      formatR_1.6         
[28] desc_1.2.0           pkgload_1.0.2        fs_1.3.1            
[31] digest_0.6.19        stringi_1.4.3        processx_3.3.1      
[34] rprojroot_1.3-2      cli_1.1.0            tools_3.5.2         
[37] magrittr_1.5         lazyeval_0.2.2       tibble_2.1.1        
[40] futile.options_1.0.1 crayon_1.3.4         whisker_0.3-2       
[43] pkgconfig_2.0.2      prettyunits_1.0.2    assertthat_0.2.1    
[46] rmarkdown_1.12       R6_2.4.0             git2r_0.25.2        
[49] compiler_3.5.2