Last updated: 2020-05-07

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Knit directory: Comparative_APA/analysis/

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Unstaged changes:
    Modified:   analysis/DeandNumPAS.Rmd
    Modified:   analysis/DirSelectionKhan.Rmd
    Modified:   analysis/ExploredAPA.Rmd
    Modified:   analysis/MMExpreiment.Rmd
    Modified:   analysis/OppositeMap.Rmd
    Modified:   analysis/PTM_analysis.Rmd
    Modified:   analysis/TotalDomStructure.Rmd
    Modified:   analysis/TotalVNuclearBothSpecies.Rmd
    Modified:   analysis/annotationInfo.Rmd
    Modified:   analysis/changeMisprimcut.Rmd
    Modified:   analysis/comp2apaQTLPAS.Rmd
    Modified:   analysis/correlationPhenos.Rmd
    Modified:   analysis/establishCutoffs.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/investigatePantro5.Rmd
    Modified:   analysis/mRNADecay.Rmd
    Modified:   analysis/multiMap.Rmd
    Modified:   analysis/pol2.Rmd
    Modified:   analysis/speciesSpecific.Rmd

Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.


These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.

File Version Author Date Message
Rmd 341a5c0 brimittleman 2020-05-07 add seperation with dapa and dic

library(workflowr)
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library(tidyverse)
── Attaching packages ──────────────────────────────────────────────────────── tidyverse 1.2.1 ──
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✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
library(cowplot)

Attaching package: 'cowplot'
The following object is masked from 'package:ggplot2':

    ggsave

I want to look at regulatory phenotype regulation based on dAPA, both, or dIC.

For this analysis I will use dIC at 5% FDR. Numbers are smaller but overlaps suggest it is more biological.

I will look at genes tested in all analysis then proportion results to only dAPA, dIC and dAPA, or dIC only. I will test for enrichement in each of these sets with expression, translation, and protein.

Load APA data:

For apa I reduce to gene level and count it as sig if at least one PAS is different.

Meta=read.table("../data/PAS_doubleFilter/PAS_5perc_either_HumanCoord_BothUsage_meta_doubleFilter.txt", header = T, stringsAsFactors = F) 


Meta_genes= Meta %>% select(gene) %>% unique()

Meta_PAS=Meta %>%  select(PAS,gene)

dAPAGenes=read.table("../data/DiffIso_Nuclear_DF/SignifianceEitherGENES_Nuclear.txt", header = T, stringsAsFactors = F)
dAPAPAS=read.table("../data/DiffIso_Nuclear_DF/AllPAS_withGeneSig.txt", header = T, stringsAsFactors = F) %>% inner_join(Meta, by=c("chr","start", "end","gene")) %>% select(PAS,gene,SigPAU2 ) 

dAPAPAS_genes= dAPAPAS %>% select(gene) %>% unique()

dAPATestedGenes= dAPAPAS  %>% select(gene) %>% unique() %>% mutate(dAPA=ifelse(gene %in% dAPAGenes$gene,"Yes", "No")) 
dICdata= read.table("../data/IndInfoContent/SimpsonMedianSignificance.txt", header = T, stringsAsFactors = F)%>% select(sIC,gene)
dAPAandDic= dICdata %>% inner_join(dAPATestedGenes,by="gene") %>% mutate(Both=ifelse(sIC=="Yes" & dAPA=="Yes", "Yes","No"),OnlyIC=ifelse(sIC=="Yes" & dAPA=="No", "Yes","No"),OnlyAPA=ifelse(sIC=="No" & dAPA=="Yes", "Yes","No"))

nrow(dAPAandDic)
[1] 8422

Expression

nameID=read.table("../../genome_anotation_data/ensemble_to_genename.txt",sep="\t", header = T, stringsAsFactors = F) %>% dplyr::select(Gene_stable_ID, Gene.name)

DiffExp=read.table("../data/DiffExpression/DEtested_allres.txt",stringsAsFactors = F,header = F, col.names = c("Gene_stable_ID" ,"logFC" ,"AveExpr" , "t" ,  "P.Value" ,  "adj.P.Val", "B"  )) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::rename('gene'=Gene.name) %>% dplyr::select(-Gene_stable_ID) %>% mutate(DE=ifelse(adj.P.Val<.05, "Yes", "No")) %>% select(gene,DE)
DEandAPA=DiffExp %>% inner_join(dAPAandDic,by="gene")
nrow(DEandAPA)
[1] 7465

Erichment for only APA:

sets=c("OnlyAPA", "OnlyIC", "Both")
DE_pval=c()
DE_enrich=c()
x=nrow(DEandAPA %>% filter(OnlyAPA=="Yes", DE=="Yes"))
m=nrow(DEandAPA %>% filter(DE=="Yes"))
n=nrow(DEandAPA %>% filter(DE=="No"))
k=nrow(DEandAPA %>% filter(OnlyAPA=="Yes"))
N=nrow(DEandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.0005193482
DE_pval=c(DE_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 447
DE_enrich=c(DE_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.122516

Only dIC

x=nrow(DEandAPA %>% filter(OnlyIC=="Yes", DE=="Yes"))
m=nrow(DEandAPA %>% filter(DE=="Yes"))
n=nrow(DEandAPA %>% filter(DE=="No"))
k=nrow(DEandAPA %>% filter(OnlyIC=="Yes"))
N=nrow(DEandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.2216107
DE_pval=c(DE_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 154
DE_enrich=c(DE_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.052215

Both:

x=nrow(DEandAPA %>% filter(Both=="Yes", DE=="Yes"))
m=nrow(DEandAPA %>% filter(DE=="Yes"))
n=nrow(DEandAPA %>% filter(DE=="No"))
k=nrow(DEandAPA %>% filter(Both=="Yes"))
N=nrow(DEandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.02681958
DE_pval=c(DE_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 163
DE_enrich=c(DE_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.128023

All de res:

DEdf=as.data.frame(cbind(sets,DE_pval, DE_enrich)) %>% rename(Pval=DE_pval, Enrichment=DE_enrich) %>% mutate(Pheno="Expression")
DEdf
     sets                 Pval       Enrichment      Pheno
1 OnlyAPA 0.000519348163532497 1.12251636247181 Expression
2  OnlyIC    0.221610701204403 1.05221488574561 Expression
3    Both   0.0268195798877835 1.12802297586811 Expression

Translation

Ribo=read.table("../data/Wang_ribo/Additionaltable5_translationComparisons.txt",header = T, stringsAsFactors = F) %>% rename("Gene_stable_ID"= ENSG) %>% inner_join(nameID,by="Gene_stable_ID") %>% dplyr::select(Gene.name, HvC.beta, HvC.pvalue, HvC.FDR) %>% rename("gene"=Gene.name) %>% mutate(dTE=ifelse(HvC.FDR <0.05, "Yes","No"))
RiboSmall= Ribo %>% select(gene,dTE)
DTandAPA=Ribo %>% inner_join(dAPAandDic,by="gene")
nrow(DTandAPA)
[1] 6477
#sets=c("OnlyAPA", "OnlyIC", "Both")
DT_pval=c()
DT_enrich=c()

only APA

x=nrow(DTandAPA %>% filter(OnlyAPA=="Yes", dTE=="Yes"))
m=nrow(DTandAPA %>% filter(dTE=="Yes"))
n=nrow(DTandAPA %>% filter(dTE=="No"))
k=nrow(DTandAPA %>% filter(OnlyAPA=="Yes"))
N=nrow(DTandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.06327494
DT_pval=c(DT_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 210
DT_enrich=c(DT_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.093646

Only dIC

x=nrow(DTandAPA %>% filter(OnlyIC=="Yes", dTE=="Yes"))
m=nrow(DTandAPA %>% filter(dTE=="Yes"))
n=nrow(DTandAPA %>% filter(dTE=="No"))
k=nrow(DTandAPA %>% filter(OnlyIC=="Yes"))
N=nrow(DTandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.02205198
DT_pval=c(DT_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 94
DT_enrich=c(DT_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.205226
x=nrow(DTandAPA %>% filter(Both=="Yes", dTE=="Yes"))
m=nrow(DTandAPA %>% filter(dTE=="Yes"))
n=nrow(DTandAPA %>% filter(dTE=="No"))
k=nrow(DTandAPA %>% filter(Both=="Yes"))
N=nrow(DTandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.01134051
DT_pval=c(DT_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 91
DT_enrich=c(DT_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.240121
DTdf=as.data.frame(cbind(sets,DT_pval, DT_enrich)) %>% rename(Pval=DT_pval, Enrichment=DT_enrich) %>% mutate(Pheno="Translation")
DTdf
     sets               Pval       Enrichment       Pheno
1 OnlyAPA 0.0632749366195107 1.09364622715088 Translation
2  OnlyIC 0.0220519791477263 1.20522601526234 Translation
3    Both 0.0113405052499701 1.24012060208466 Translation

Protein

(pval is adjusted already)

Prot= read.table("../data/Khan_prot/ProtData_effectSize.txt",header = T,stringsAsFactors = F)  %>% mutate(dP=ifelse(pval<0.05, "Yes", "No"))


ProtSmall=Prot %>% select(gene, dP)
DPandAPA=Prot %>% inner_join(dAPAandDic,by="gene")
nrow(DPandAPA)
[1] 2641
#sets=c("OnlyAPA", "OnlyIC", "Both")
DP_pval=c()
DP_enrich=c()

only APA

x=nrow(DPandAPA %>% filter(OnlyAPA=="Yes", dP=="Yes"))
m=nrow(DPandAPA %>% filter(dP=="Yes"))
n=nrow(DPandAPA %>% filter(dP=="No"))
k=nrow(DPandAPA %>% filter(OnlyAPA=="Yes"))
N=nrow(DPandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.2293006
DP_pval=c(DP_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 130
DP_enrich=c(DP_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 1.052798

Only dIC

x=nrow(DPandAPA %>% filter(OnlyIC=="Yes", dP=="Yes"))
m=nrow(DPandAPA %>% filter(dP=="Yes"))
n=nrow(DPandAPA %>% filter(dP=="No"))
k=nrow(DPandAPA %>% filter(OnlyIC=="Yes"))
N=nrow(DPandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.8222889
DP_pval=c(DP_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 68
DP_enrich=c(DP_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 0.925635
x=nrow(DPandAPA %>% filter(Both=="Yes", dP=="Yes"))
m=nrow(DPandAPA %>% filter(dP=="Yes"))
n=nrow(DPandAPA %>% filter(dP=="No"))
k=nrow(DPandAPA %>% filter(Both=="Yes"))
N=nrow(DPandAPA)
phyper(x-1,m,n,k,lower.tail=F)
[1] 0.8802321
DP_pval=c(DP_pval, phyper(x-1,m,n,k,lower.tail=F))
x
[1] 56
DP_enrich=c(DP_enrich, (x/k)/(m/N))
(x/k)/(m/N)
[1] 0.895688
DPdf=as.data.frame(cbind(sets,DP_pval, DP_enrich)) %>% rename(Pval=DP_pval, Enrichment=DP_enrich) %>% mutate(Pheno="Protein")
DPdf
     sets              Pval        Enrichment   Pheno
1 OnlyAPA 0.229300585846805  1.05279781179472 Protein
2  OnlyIC 0.822288948709401 0.925634999175326 Protein
3    Both 0.880232087900127 0.895687984496124 Protein

Plot together:

AllDF= DEdf %>% bind_rows(DTdf) %>% bind_rows(DPdf)
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
Warning in bind_rows_(x, .id): Unequal factor levels: coercing to character
Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector

Warning in bind_rows_(x, .id): binding character and factor vector,
coercing into character vector
AllDF$Pval=as.numeric(AllDF$Pval)
AllDF$Enrichment=as.numeric(AllDF$Enrichment)
AllDF$Pheno=factor(AllDF$Pheno, levels=c("Expression", "Translation", "Protein"))
useCOl <- c("#d73027", "#4575b4","#fee090")

enrichplot=ggplot(AllDF,aes(x=Pheno, by=sets, y=Enrichment,fill=sets)) +geom_bar(stat = "identity",position = "dodge") +geom_hline(yintercept =1) + scale_fill_manual(values=useCOl)

enrichplot

enrichpoint=ggplot(AllDF,aes(x=sets,col=sets,y=Enrichment,label = round(Enrichment,3)))+ geom_bar(stat="identity",color="grey",aes(y=AllDF$Enrichment),width=.01)+geom_point(size=10) + coord_flip() + geom_hline(yintercept = 1) + facet_grid(~Pheno)+scale_color_manual(values=useCOl)+ labs( title="Enrichment for APA phenotype differences in other regulatory phenotypes",x="Set", y="Enrichement")+geom_text(color = "black", size = 3) + theme(legend.position = "none")


enrichpoint

pvalplot=ggplot(AllDF,aes(x=Pheno, by=sets, y=-log10(Pval),fill=sets)) +geom_bar(stat = "identity",position = "dodge") +geom_hline(yintercept =1.3)+ scale_fill_manual(values=useCOl)+  theme(legend.position = "bottom")

pvalplot

plot together:

plot_grid(enrichpoint,pvalplot, nrow=2)


sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)

Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] cowplot_0.9.4   forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1  
 [5] purrr_0.3.2     readr_1.3.1     tidyr_0.8.3     tibble_2.1.1   
 [9] ggplot2_3.1.1   tidyverse_1.2.1 workflowr_1.6.0

loaded via a namespace (and not attached):
 [1] tidyselect_0.2.5 reshape2_1.4.3   haven_1.1.2      lattice_0.20-38 
 [5] colorspace_1.3-2 generics_0.0.2   htmltools_0.3.6  yaml_2.2.0      
 [9] rlang_0.4.0      later_0.7.5      pillar_1.3.1     glue_1.3.0      
[13] withr_2.1.2      modelr_0.1.2     readxl_1.1.0     plyr_1.8.4      
[17] munsell_0.5.0    gtable_0.2.0     cellranger_1.1.0 rvest_0.3.2     
[21] evaluate_0.12    labeling_0.3     knitr_1.20       httpuv_1.4.5    
[25] broom_0.5.1      Rcpp_1.0.4.6     promises_1.0.1   scales_1.0.0    
[29] backports_1.1.2  jsonlite_1.6     fs_1.3.1         hms_0.4.2       
[33] digest_0.6.18    stringi_1.2.4    grid_3.5.1       rprojroot_1.3-2 
[37] cli_1.1.0        tools_3.5.1      magrittr_1.5     lazyeval_0.2.1  
[41] crayon_1.3.4     whisker_0.3-2    pkgconfig_2.0.2  xml2_1.2.0      
[45] lubridate_1.7.4  assertthat_0.2.0 rmarkdown_1.10   httr_1.3.1      
[49] rstudioapi_0.10  R6_2.3.0         nlme_3.1-137     git2r_0.26.1    
[53] compiler_3.5.1