list.of.packages <- c("tidyverse", "reshape2", "here", "methylKit", "ggforce", "matrixStats", "Pstat", "viridis", "plotly", "readr", "GenomicRanges", "vegan", "factoextra", "PerformanceAnalytics", "corrplot") #add new libraries here
new.packages <- list.of.packages[!(list.of.packages %in% installed.packages()[,"Package"])]
if(length(new.packages)) install.packages(new.packages)
# Load all libraries
lapply(list.of.packages, FUN = function(X) {
do.call("require", list(X))
})sessionInfo()## R version 3.5.1 (2018-07-02)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS 10.15.7
##
## 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 stats4 stats graphics grDevices utils datasets
## [8] methods base
##
## other attached packages:
## [1] corrplot_0.84 PerformanceAnalytics_2.0.4
## [3] xts_0.12-0 zoo_1.8-8
## [5] factoextra_1.0.7 vegan_2.5-6
## [7] lattice_0.20-41 permute_0.9-5
## [9] plotly_4.9.2.1 viridis_0.5.1
## [11] viridisLite_0.3.0 Pstat_1.2
## [13] matrixStats_0.56.0 ggforce_0.3.1
## [15] methylKit_1.8.1 GenomicRanges_1.34.0
## [17] GenomeInfoDb_1.18.2 IRanges_2.16.0
## [19] S4Vectors_0.20.1 BiocGenerics_0.28.0
## [21] here_0.1 reshape2_1.4.4
## [23] forcats_0.5.0 stringr_1.4.0
## [25] dplyr_0.8.5 purrr_0.3.4
## [27] readr_1.3.1 tidyr_1.0.3
## [29] tibble_3.0.1 ggplot2_3.3.0
## [31] tidyverse_1.3.0
##
## loaded via a namespace (and not attached):
## [1] colorspace_1.4-1 ellipsis_0.3.0
## [3] mclust_5.4.5 rprojroot_1.3-2
## [5] qvalue_2.14.1 XVector_0.22.0
## [7] fs_1.4.1 rstudioapi_0.11
## [9] farver_2.0.3 ggrepel_0.8.2
## [11] fansi_0.4.1 mvtnorm_1.1-0
## [13] lubridate_1.7.8 xml2_1.3.2
## [15] splines_3.5.1 R.methodsS3_1.8.0
## [17] knitr_1.28 polyclip_1.10-0
## [19] jsonlite_1.6.1 Rsamtools_1.34.1
## [21] broom_0.5.6 cluster_2.1.0
## [23] dbplyr_1.4.3 R.oo_1.23.0
## [25] compiler_3.5.1 httr_1.4.1
## [27] backports_1.1.6 lazyeval_0.2.2
## [29] assertthat_0.2.1 Matrix_1.2-18
## [31] limma_3.38.3 cli_2.0.2
## [33] tweenr_1.0.1 htmltools_0.4.0
## [35] tools_3.5.1 coda_0.19-3
## [37] gtable_0.3.0 glue_1.4.0
## [39] GenomeInfoDbData_1.2.0 Rcpp_1.0.4.6
## [41] bbmle_1.0.23.1 Biobase_2.42.0
## [43] cellranger_1.1.0 vctrs_0.3.0
## [45] Biostrings_2.50.2 nlme_3.1-143
## [47] rtracklayer_1.42.2 xfun_0.13
## [49] fastseg_1.28.0 rvest_0.3.5
## [51] lifecycle_0.2.0 gtools_3.8.2
## [53] XML_3.99-0.3 zlibbioc_1.28.0
## [55] MASS_7.3-51.6 scales_1.1.1
## [57] hms_0.5.3 SummarizedExperiment_1.12.0
## [59] yaml_2.2.1 gridExtra_2.3
## [61] emdbook_1.3.12 bdsmatrix_1.3-4
## [63] stringi_1.4.6 BiocParallel_1.16.6
## [65] rlang_0.4.6 pkgconfig_2.0.3
## [67] bitops_1.0-6 evaluate_0.14
## [69] htmlwidgets_1.5.1 GenomicAlignments_1.18.1
## [71] tidyselect_1.1.0 plyr_1.8.6
## [73] magrittr_1.5 R6_2.4.1
## [75] generics_0.0.2 DelayedArray_0.8.0
## [77] DBI_1.1.0 mgcv_1.8-31
## [79] pillar_1.4.4 haven_2.2.0
## [81] withr_2.2.0 RCurl_1.98-1.2
## [83] modelr_0.1.7 crayon_1.3.4
## [85] rmarkdown_2.1 grid_3.5.1
## [87] readxl_1.3.1 data.table_1.12.8
## [89] reprex_0.3.0 digest_0.6.25
## [91] numDeriv_2016.8-1.1 R.utils_2.9.2
## [93] munsell_0.5.0 quadprog_1.5-8getwd()## [1] "/Volumes/Bumblebee/C.magister_methyl-oa/notebooks"gannetFiles were transferred from Hyak on December 27th, 2020 using rsync.
file.list=list("/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH01-06_S1_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH01-14_S2_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH01-22_S3_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH01-38_S4_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH03-04_S5_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH03-15_S6_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH03-33_S7_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH05-01_S8_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH05-06_S9_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH05-21_S10_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH05-24_S11_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH07-06_S12_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH07-11_S13_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH07-24_S14_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH09-02_S15_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH09-13_S16_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH09-28_S17_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH10-01_S18_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH10-08_S19_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam",
"/Volumes/Bumblebee/C.magister_methyl-oa/qc-processing/MiSeq-QC/bismark/CH10-11_S20_L001_R1_001_val_1_bismark_bt2_pe.deduplicated.sorted.bam")summary <- read_delim(file="../qc-processing/MiSeq-QC/mbdall.txt", delim="\t") %>%
arrange(sample_mbd) %>% filter(sample_mbd != "NA")## Parsed with column specification:
## cols(
## .default = col_double(),
## sample = col_character(),
## Low_CpGmeth = col_character(),
## treatment = col_character(),
## treatment_high_lowCO2 = col_character(),
## developmental_stage = col_character(),
## notes = col_character(),
## DNAiso_batch = col_character(),
## `pool for library?` = col_character()
## )## See spec(...) for full column specifications.head(summary)## # A tibble: 6 x 30
## sample sample_mbd Low_CpGmeth tank treatment treatment_high_…
## <chr> <dbl> <chr> <dbl> <chr> <chr>
## 1 CH01-… 1 no 3 LC L
## 2 CH01-… 2 no 3 LC L
## 3 CH01-… 3 no 1 LB L
## 4 CH01-… 4 no 1 LB L
## 5 CH03-… 5 yes 1 LB L
## 6 CH03-… 6 yes 1 LB L
## # … with 24 more variables: developmental_stage <chr>, notes <chr>,
## # DNAiso_batch <chr>, conc_ng.uL <dbl>, yield_ug <dbl>,
## # MBD_concentration_ng.uL <dbl>, Total_recovery_ng <dbl>,
## # Percent_recovery <dbl>, MBD_date <dbl>,
## # library_bioanlyzer_mean_fragment_size_bp <dbl>,
## # library_bioanalyzer_molarity_pmol.L <dbl>, `pool for library?` <chr>,
## # qubit_concentration_ng.uL <dbl>, qubit_molarity_nM <dbl>,
## # library_4nM_uL <dbl>, Total_Reads <dbl>, Aligned_Reads <dbl>,
## # Unaligned_Reads <dbl>, Ambiguously_Aligned_Reads <dbl>, Unique_reads <dbl>,
## # perc_totalread_unique <dbl>, CpGs_Meth <dbl>, CHGs_Meth <dbl>,
## # CHHs_Meth <dbl>cor(summary %>% dplyr::select_if(is.numeric)) %>% corrplot(tl.cex=.45)