Last updated: 2021-02-15

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Introduction

In the GEO submission 2 processed files were uploaded.

  1. mrna_fulllen_pe_strrev_q30.mx.AAV_PR.unfiltered
  2. mrna_fulllen_pe_strrev_q30.mx.AAV_PR.fix_filt

They have been uploaded in the /output folder and will be used below to generate different figures.

Used libraries and functions

library(edgeR)
Loading required package: limma
library(limma)
library(Glimma)
library(gplots)

Attaching package: 'gplots'
The following object is masked from 'package:stats':

    lowess
library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.0.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference

If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional 
  genomic data. Bioinformatics 2016.
========================================
library(circlize)
========================================
circlize version 0.4.10
CRAN page: https://cran.r-project.org/package=circlize
Github page: https://github.com/jokergoo/circlize
Documentation: https://jokergoo.github.io/circlize_book/book/

If you use it in published research, please cite:
Gu, Z. circlize implements and enhances circular visualization
  in R. Bioinformatics 2014.

This message can be suppressed by:
  suppressPackageStartupMessages(library(circlize))
========================================
library(RColorBrewer)
library(mclust)
Package 'mclust' version 5.4.6
Type 'citation("mclust")' for citing this R package in publications.

Read files

rm1 <- read.delim("/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Mouse_AAV_PGR_RNAseq_bulk/output/mrna_fulllen_pe_strrev_q30.mx.AAV_PR.fix_filt", row.names = 1)
colnames(rm1) = gsub("AAV.","",colnames(rm1))

info = read.delim("/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Mouse_AAV_PGR_RNAseq_bulk/output/2020021_AAV_PR_RNA_samplesheet.txt", header = TRUE, sep = "\t")
info$ID = gsub("_",".",info$ID)

names(rm1) = info$ID[match(names(rm1),info$ID)]

m = match(info$ID,names(rm1))
rm2 = rm1[,m]
rm1 = rm2


sampleinfo = info
levels(factor(sampleinfo$Group))
[1] "MCS" "PR" 
levels(factor(sampleinfo$BinSex))
[1] "MCS_F" "MCS_M" "PR_F"  "PR_M" 
sampleinfo$colour = c("springgreen3","purple")[factor(sampleinfo$Group)]
table(colnames(rm2)==sampleinfo$ID)

TRUE 
  13 
y <- DGEList(rm2)

Make plot

par(mfrow=c(1,3))

plotMDS(y, pch=c(0,1)[factor(sampleinfo$Group)], col=sampleinfo$colour,dim.plot = c(1,3), cex = 2)
legend("top", legend = c("AAV_MCS","AAV_PR"), pch=c(1,0), col = c("purple", "springgreen3"), cex=1)

plotMDS(y, pch=c(0,15,1,16)[factor(sampleinfo$BinSex)], col=sampleinfo$colour, dim.plot = c(1,3),cex = 2)
legend("top", legend = c("AAV_MCS","AAV_PR"), pch=c(1,0), col = c("purple", "springgreen3"), cex=1)
legend("topleft", legend = c("F","M"), pch=c(1,16), col = c("grey"), cex=1)

plotMDS(y, cex = 0.8, dim.plot = c(1,3))

Version Author Date
e1cb83f evangelynsim 2021-02-15

Remove Chr X & Y genes

rm3 = read.delim("/group/card2/Evangelyn_Sim/Transcriptome_chromatin_human/Sequencing_ATAC_RNA/GITHUB/Mouse_AAV_PGR_RNAseq_bulk/output/mrna_fulllen_pe_strrev_q30.mx.chr", header = TRUE, row.names = 1)
rm3 = merge(rm3, rm2, by = "row.names")
rm3 = rm3[!grepl("Y",rm3$Chr),]
rm3 = rm3[!grepl("X",rm3$Chr),]
row.names(rm3)= rm3$Row.names
rm3 = rm3[,c(7:ncol(rm3))]
rm2 = rm3

z <- DGEList(rm3)

Make MDS plot (removed Chr X & Y genes)

par(mfrow=c(1,3))

plotMDS(z, pch=c(0,1)[factor(sampleinfo$Group)], col=sampleinfo$colour,dim.plot = c(1,3), cex = 2)
legend("left", legend = c("AAV_MCS","AAV_PR"), pch=c(1,0), col = c("purple", "springgreen3"), cex=1)

plotMDS(z, pch=c(0,15,1,16)[factor(sampleinfo$BinSex)], col=sampleinfo$colour, dim.plot = c(1,3),cex = 2)
legend("left", legend = c("AAV_MCS","AAV_PR"), pch=c(1,0), col = c("purple", "springgreen3"), cex=1)
legend("topleft", legend = c("F","M"), pch=c(1,16), col = c("grey"), cex=1)

plotMDS(z, cex = 0.8, dim.plot = c(1,3))

Version Author Date
e1cb83f evangelynsim 2021-02-15 

sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS:   /hpc/software/installed/R/3.6.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/installed/R/3.6.1/lib64/R/lib/libRlapack.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] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] mclust_5.4.6         RColorBrewer_1.1-2   circlize_0.4.10     
[4] ComplexHeatmap_2.0.0 gplots_3.1.0         Glimma_1.12.0       
[7] edgeR_3.26.8         limma_3.40.6         workflowr_1.6.2     

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.5          pillar_1.4.6        compiler_3.6.1     
 [4] later_1.1.0.1       git2r_0.27.1        highr_0.8          
 [7] bitops_1.0-6        tools_3.6.1         digest_0.6.27      
[10] clue_0.3-57         jsonlite_1.7.0      evaluate_0.14      
[13] lifecycle_0.2.0     tibble_3.0.3        lattice_0.20-41    
[16] png_0.1-7           pkgconfig_2.0.3     rlang_0.4.7        
[19] rstudioapi_0.11     parallel_3.6.1      yaml_2.2.1         
[22] xfun_0.18           cluster_2.1.0       stringr_1.4.0      
[25] knitr_1.30          GlobalOptions_0.1.2 caTools_1.18.0     
[28] gtools_3.8.2        fs_1.5.0            vctrs_0.3.2        
[31] locfit_1.5-9.4      rprojroot_1.3-2     glue_1.4.2         
[34] R6_2.5.0            GetoptLong_1.0.2    rmarkdown_2.5      
[37] magrittr_1.5        whisker_0.4         backports_1.1.10   
[40] promises_1.1.1      ellipsis_0.3.1      htmltools_0.5.0    
[43] shape_1.4.4         colorspace_1.4-1    httpuv_1.5.4       
[46] KernSmooth_2.23-17  stringi_1.5.3       rjson_0.2.20       
[49] crayon_1.3.4