mouse-chronic-ccl4
christianholland
2020-12-18
Last updated: 2020-12-18
Checks: 7 0
Knit directory: meta-liver/
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|---|---|---|---|---|
| Rmd | 261f1a4 | christianholland | 2020-12-18 | Start my new project |
Introduction
TODO
Libraries and sources
These libraries and sources are used in this analysis
library(tidyverse)
library(tidylog)
library(here)
library(edgeR)
#> Warning: package 'edgeR' was built under R version 4.0.3
#> Warning: package 'limma' was built under R version 4.0.3
options("tidylog.display" = list(print))
source(here("code/utils-rnaseq.R"))
source(here("code/utils-wrapper.R"))
source(here("code/utils-plots.R"))Analysis specific options
# i/o
data_path = "data/mouse-chronic-ccl4"
output_path = "output/mouse-chronic-ccl4"
figure_path = "output/mouse-chronic-ccl4/figures"
# graphical parameters
# fontsize
fz = 9Preliminary exploratory analysis
PCA of raw data
count_matrix = readRDS(here(data_path, "count_matrix.rds"))
meta = readRDS(here(data_path, "meta_data.rds"))
stopifnot(colnames(count_matrix) == meta$sample)
# remove constant expressed genes and transform to log2 scale
preprocessed_count_matrix = preprocess_count_matrix(count_matrix)
#> Discarding 7711 genes
#> Keeping 24833 genes
pca_result = do_pca(preprocessed_count_matrix, meta, top_n_var_genes = 2000)
#> left_join: added 3 columns (time, treatment, group)
#> > rows only in x 0
#> > rows only in y ( 0)
#> > matched rows 36
#> > ====
#> > rows total 36
plot_pca(pca_result, feature = "time") +
my_theme()
plot_pca(pca_result, feature = "treatment") +
my_theme()
Data processing
Normalization
count_matrix = readRDS(here(data_path, "count_matrix.rds"))
meta = readRDS(here(data_path, "meta_data.rds"))
stopifnot(meta$sample == colnames(count_matrix))
dge_obj = DGEList(count_matrix, group = meta$group)
# filter low read counts, TMM normalization and logCPM transformation
norm = voom_normalization(dge_obj)
#> Discarding 17206 genes
#> Keeping 15338 genes
saveRDS(norm, here(output_path, "normalized_expression.rds"))PCA of normalized data
expr = readRDS(here(output_path, "normalized_expression.rds"))
meta = readRDS(here(data_path, "meta_data.rds"))
pca_result = do_pca(expr, meta, top_n_var_genes = 1000)
#> left_join: added 3 columns (time, treatment, group)
#> > rows only in x 0
#> > rows only in y ( 0)
#> > matched rows 36
#> > ====
#> > rows total 36
saveRDS(pca_result, here(output_path, "pca_result.rds"))
### PC1 vs PC2
plot_pca(pca_result, feature = "time") +
my_theme()
plot_pca(pca_result, feature = "treatment") +
my_theme()
sessionInfo()
#> R version 4.0.2 (2020-06-22)
#> Platform: x86_64-apple-darwin17.0 (64-bit)
#> Running under: macOS Mojave 10.14.5
#>
#> Matrix products: default
#> BLAS: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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 datasets utils methods base
#>
#> other attached packages:
#> [1] edgeR_3.32.0 limma_3.46.0 here_1.0.1 tidylog_1.0.2
#> [5] forcats_0.5.0 stringr_1.4.0 dplyr_1.0.2 purrr_0.3.4
#> [9] readr_1.4.0 tidyr_1.1.2 tibble_3.0.4 ggplot2_3.3.2
#> [13] tidyverse_1.3.0 workflowr_1.6.2
#>
#> loaded via a namespace (and not attached):
#> [1] Rcpp_1.0.5 locfit_1.5-9.4 lubridate_1.7.9.2 lattice_0.20-41
#> [5] clisymbols_1.2.0 assertthat_0.2.1 rprojroot_2.0.2 digest_0.6.27
#> [9] R6_2.5.0 cellranger_1.1.0 backports_1.2.1 reprex_0.3.0
#> [13] evaluate_0.14 httr_1.4.2 pillar_1.4.7 rlang_0.4.9
#> [17] readxl_1.3.1 rstudioapi_0.13 whisker_0.4 rmarkdown_2.6
#> [21] labeling_0.4.2 munsell_0.5.0 broom_0.7.3 compiler_4.0.2
#> [25] httpuv_1.5.4 modelr_0.1.8 xfun_0.19 pkgconfig_2.0.3
#> [29] htmltools_0.5.0 tidyselect_1.1.0 viridisLite_0.3.0 fansi_0.4.1
#> [33] crayon_1.3.4 dbplyr_2.0.0 withr_2.3.0 later_1.1.0.1
#> [37] grid_4.0.2 jsonlite_1.7.2 gtable_0.3.0 lifecycle_0.2.0
#> [41] DBI_1.1.0 git2r_0.27.1 magrittr_2.0.1 scales_1.1.1
#> [45] cli_2.2.0 stringi_1.5.3 farver_2.0.3 renv_0.12.3
#> [49] fs_1.5.0 promises_1.1.1 xml2_1.3.2 ellipsis_0.3.1
#> [53] generics_0.1.0 vctrs_0.3.6 cowplot_1.1.0 tools_4.0.2
#> [57] glue_1.4.2 hms_0.5.3 yaml_2.2.1 colorspace_2.0-0
#> [61] rvest_0.3.6 knitr_1.30 haven_2.3.1