Last updated: 2019-04-25

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Knit directory: apaQTL/analysis/

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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 48b2ec1 brimittleman 2019-04-25 add map befroe mp filter
html be227e7 brimittleman 2019-04-25 Build site.
Rmd 6cb0a99 brimittleman 2019-04-25 add seq meta pltos

In this analysis I want to compare the sequencing depth between batches.

library(tidyverse)
── Attaching packages ──────────────────────────────────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 3.1.0       ✔ purrr   0.3.2  
✔ tibble  2.1.1       ✔ dplyr   0.8.0.1
✔ tidyr   0.8.3       ✔ stringr 1.3.1  
✔ readr   1.3.1       ✔ forcats 0.3.0  
── Conflicts ─────────────────────────────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Load metadata:

metadata=read.table("../data/MetaDataSequencing.txt",header = T)
meta_T=metadata %>% filter(grepl("T", Sample_ID)) %>% mutate(samp=paste("X", Sample_ID, sep=""))
meta_N=metadata %>% filter(grepl("N", Sample_ID)) %>%  mutate(samp=paste("X", Sample_ID, sep=""))

Read count

metadata$batch=as.factor(metadata$batch)
ggplot(metadata, aes(x=batch, group=batch, y=reads, fill=batch)) + geom_boxplot() + geom_jitter() + facet_grid(~fraction) + labs(title="Read count by batch")

Version Author Date
be227e7 brimittleman 2019-04-25

Mapped reads

ggplot(metadata, aes(x=batch, group=batch, y=prop_MappedwithoutMP, fill=batch)) + geom_boxplot() + geom_jitter() + facet_grid(~fraction) + labs(title="Mapped reads by batch")

Version Author Date
be227e7 brimittleman 2019-04-25

Map prop

ggplot(metadata, aes(x=batch, group=batch, y=prop_MappedwithoutMP, fill=batch)) + geom_boxplot() + geom_jitter() + facet_grid(~fraction) + labs(title="Proportion Mapped reads by batch")

Version Author Date
be227e7 brimittleman 2019-04-25

Library concentration

ggplot(metadata, aes(x=batch, group=batch, y=library_conc, fill=batch)) + geom_boxplot() + geom_jitter() + facet_grid(~fraction) + labs(title="Library concentrations by batch")

Version Author Date
be227e7 brimittleman 2019-04-25

before mp

ggplot(metadata, aes(x=batch, group=batch, y=mapped, fill=batch)) + geom_boxplot() + geom_jitter() + facet_grid(~fraction) + labs(title="Mapped reads before MP filter by batch")


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] forcats_0.3.0   stringr_1.3.1   dplyr_0.8.0.1   purrr_0.3.2    
[5] readr_1.3.1     tidyr_0.8.3     tibble_2.1.1    ggplot2_3.1.0  
[9] tidyverse_1.2.1

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0       cellranger_1.1.0 pillar_1.3.1     compiler_3.5.1  
 [5] git2r_0.23.0     plyr_1.8.4       workflowr_1.3.0  tools_3.5.1     
 [9] digest_0.6.18    lubridate_1.7.4  jsonlite_1.6     evaluate_0.12   
[13] nlme_3.1-137     gtable_0.2.0     lattice_0.20-38  pkgconfig_2.0.2 
[17] rlang_0.3.1      cli_1.0.1        rstudioapi_0.10  yaml_2.2.0      
[21] haven_1.1.2      withr_2.1.2      xml2_1.2.0       httr_1.3.1      
[25] knitr_1.20       hms_0.4.2        generics_0.0.2   fs_1.2.6        
[29] rprojroot_1.3-2  grid_3.5.1       tidyselect_0.2.5 glue_1.3.0      
[33] R6_2.3.0         readxl_1.1.0     rmarkdown_1.10   reshape2_1.4.3  
[37] modelr_0.1.2     magrittr_1.5     whisker_0.3-2    backports_1.1.2 
[41] scales_1.0.0     htmltools_0.3.6  rvest_0.3.2      assertthat_0.2.0
[45] colorspace_1.3-2 labeling_0.3     stringi_1.2.4    lazyeval_0.2.1  
[49] munsell_0.5.0    broom_0.5.1      crayon_1.3.4