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| library("BiocFileCache") | |
| library("SummarizedExperiment") | |
| library("googlesheets4") | |
| ## Location for temporarely downloading the files | |
| bfc_temp <- BiocFileCache(tempdir()) | |
| ## Download the BSP1 and BSP2 data | |
| bsp1_data <- bfcrpath(bfc_temp, "https://s3.us-east-2.amazonaws.com/jaffe-nat-neuro-2018/rse_gene_BrainSeq_Phase1_hg19_TopHat2_EnsemblV75.rda") | |
| bsp2_data <- bfcrpath(bfc_temp, "https://s3.us-east-2.amazonaws.com/libd-brainseq2/rse_gene_unfiltered.Rdata") | |
| ## For BSP1, use the data at JHPCE with the MDD and BPD samples | |
| bsp1_data <- "/dcl01/ajaffe/data/lab/brainseq_phase1/count_data/dlpfc_polyA_brainseq_phase1_hg38_rseGene_merged_n732.rda" | |
| ## Same file as the one available on the web for BSP2 | |
| bsp2_data <- "/dcl01/lieber/ajaffe/lab/brainseq_phase2/expr_cutoff/unfiltered/rse_gene_unfiltered.Rdata" | |
| ## Load into R | |
| load(bsp1_data, verbose = TRUE) | |
| rse_bsp1 <- rse_gene | |
| load(bsp2_data, verbose = TRUE) | |
| rse_bsp2 <- rse_gene | |
| ## Explore how the data is labeled | |
| colnames(colData(rse_bsp1)) | |
| colnames(colData(rse_bsp2)) | |
| ## Extract a few variables of interest | |
| meta_bsp1 <- with(colData(rse_bsp1), data.frame( | |
| "BrainID" = BrNum, | |
| "SampleID" = RNum, | |
| "Diagnosis" = Dx, | |
| "Age" = Age, | |
| "Sex" = Sex, | |
| "Region" = "DLPFC", | |
| "RNAseqDataAvailable" = TRUE, | |
| "GenotypingPlatform" = NA, | |
| "Phase" = "BSP1", | |
| "GenotypeRegion" = NA, | |
| "IDAT_prefix" = NA | |
| )) | |
| meta_bsp2 <- with(colData(rse_bsp2), data.frame( | |
| "BrainID" = BrNum, | |
| "SampleID" = RNum, | |
| "Diagnosis" = Dx, | |
| "Age" = Age, | |
| "Sex" = Sex, | |
| "Region" = Region, | |
| "RNAseqDataAvailable" = TRUE, | |
| "GenotypingPlatform" = NA, | |
| "Phase" = "BSP2", | |
| "GenotypeRegion" = NA, | |
| "IDAT_prefix" = NA | |
| )) | |
| ## Combine | |
| meta_both <- rbind(meta_bsp1, meta_bsp2) | |
| ## Share | |
| ss <- gs4_create( | |
| "BSP1_BSP2_samples" | |
| ) | |
| sheet_write(meta_both, ss = "1BAEJcjUM5qfFdFSAoo7bToFgaWHdNd6YjLd0NYkWjHw") | |
| with(meta_both, table(Diagnosis, Phase)) | |
| # Phase | |
| # Diagnosis BSP1 BSP2 | |
| # Bipolar 67 0 | |
| # Control 336 614 | |
| # MDD 150 0 | |
| # Schizo 179 286 | |
| ## View data at https://docs.google.com/spreadsheets/d/1BAEJcjUM5qfFdFSAoo7bToFgaWHdNd6YjLd0NYkWjHw/edit?usp=sharing | |
| ## Reproducibility information | |
| options(width = 120) | |
| sessioninfo::session_info() | |
| # - Session info ------------------------------------------------------------------------------------------------------- | |
| # setting value | |
| # version R version 4.0.2 (2020-06-22) | |
| # os Windows 10 x64 | |
| # system x86_64, mingw32 | |
| # ui RStudio | |
| # language (EN) | |
| # collate English_United States.1252 | |
| # ctype English_United States.1252 | |
| # tz America/New_York | |
| # date 2020-10-19 | |
| # | |
| # - Packages ----------------------------------------------------------------------------------------------------------- | |
| # package * version date lib source | |
| # askpass 1.1 2019-01-13 [1] CRAN (R 4.0.2) | |
| # assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2) | |
| # backports 1.1.10 2020-09-15 [1] CRAN (R 4.0.2) | |
| # Biobase * 2.48.0 2020-04-27 [1] Bioconductor | |
| # BiocFileCache * 1.12.1 2020-08-04 [1] Bioconductor | |
| # BiocGenerics * 0.34.0 2020-04-27 [1] Bioconductor | |
| # bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2) | |
| # bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2) | |
| # bitops 1.0-6 2013-08-17 [1] CRAN (R 4.0.0) | |
| # blob 1.2.1 2020-01-20 [1] CRAN (R 4.0.2) | |
| # callr 3.5.1 2020-10-13 [1] CRAN (R 4.0.2) | |
| # cellranger 1.1.0 2016-07-27 [1] CRAN (R 4.0.2) | |
| # cli 2.1.0 2020-10-12 [1] CRAN (R 4.0.2) | |
| # crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2) | |
| # curl 4.3 2019-12-02 [1] CRAN (R 4.0.2) | |
| # DBI 1.1.0 2019-12-15 [1] CRAN (R 4.0.2) | |
| # dbplyr * 1.4.4 2020-05-27 [1] CRAN (R 4.0.2) | |
| # DelayedArray * 0.14.1 2020-07-15 [1] Bioconductor | |
| # desc 1.2.0 2018-05-01 [1] CRAN (R 4.0.2) | |
| # devtools * 2.3.2 2020-09-18 [1] CRAN (R 4.0.2) | |
| # digest 0.6.25 2020-02-23 [1] CRAN (R 4.0.2) | |
| # dplyr 1.0.2 2020-08-18 [1] CRAN (R 4.0.2) | |
| # ellipsis 0.3.1 2020-05-15 [1] CRAN (R 4.0.2) | |
| # fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2) | |
| # fs 1.5.0 2020-07-31 [1] CRAN (R 4.0.2) | |
| # gargle 0.5.0 2020-05-06 [1] CRAN (R 4.0.2) | |
| # generics 0.0.2 2018-11-29 [1] CRAN (R 4.0.2) | |
| # GenomeInfoDb * 1.24.2 2020-06-15 [1] Bioconductor | |
| # GenomeInfoDbData 1.2.3 2020-06-30 [1] Bioconductor | |
| # GenomicRanges * 1.40.0 2020-04-27 [1] Bioconductor | |
| # glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2) | |
| # googledrive 1.0.1 2020-05-05 [1] CRAN (R 4.0.2) | |
| # googlesheets4 * 0.2.0 2020-05-08 [1] CRAN (R 4.0.2) | |
| # here 0.1 2017-05-28 [1] CRAN (R 4.0.2) | |
| # httr 1.4.2 2020-07-20 [1] CRAN (R 4.0.2) | |
| # IRanges * 2.22.2 2020-05-21 [1] Bioconductor | |
| # jsonlite 1.7.1 2020-09-07 [1] CRAN (R 4.0.2) | |
| # lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.2) | |
| # lifecycle 0.2.0 2020-03-06 [1] CRAN (R 4.0.2) | |
| # magrittr 1.5 2014-11-22 [1] CRAN (R 4.0.2) | |
| # Matrix 1.2-18 2019-11-27 [1] CRAN (R 4.0.2) | |
| # matrixStats * 0.57.0 2020-09-25 [1] CRAN (R 4.0.2) | |
| # memoise 1.1.0 2017-04-21 [1] CRAN (R 4.0.2) | |
| # openssl 1.4.3 2020-09-18 [1] CRAN (R 4.0.2) | |
| # pillar 1.4.6 2020-07-10 [1] CRAN (R 4.0.2) | |
| # pkgbuild 1.1.0 2020-07-13 [1] CRAN (R 4.0.2) | |
| # pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.0.2) | |
| # pkgload 1.1.0 2020-05-29 [1] CRAN (R 4.0.2) | |
| # prettyunits 1.1.1 2020-01-24 [1] CRAN (R 4.0.2) | |
| # processx 3.4.4 2020-09-03 [1] CRAN (R 4.0.2) | |
| # ps 1.3.4 2020-08-11 [1] CRAN (R 4.0.2) | |
| # purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2) | |
| # R6 2.4.1 2019-11-12 [1] CRAN (R 4.0.2) | |
| # rappdirs 0.3.1 2016-03-28 [1] CRAN (R 4.0.2) | |
| # Rcpp 1.0.5 2020-07-06 [1] CRAN (R 4.0.2) | |
| # RCurl 1.98-1.2 2020-04-18 [1] CRAN (R 4.0.0) | |
| # remotes 2.2.0 2020-07-21 [1] CRAN (R 4.0.2) | |
| # rlang 0.4.7 2020-07-09 [1] CRAN (R 4.0.2) | |
| # rprojroot 1.3-2 2018-01-03 [1] CRAN (R 4.0.2) | |
| # RSQLite 2.2.1 2020-09-30 [1] CRAN (R 4.0.2) | |
| # rstudioapi 0.11 2020-02-07 [1] CRAN (R 4.0.2) | |
| # S4Vectors * 0.26.1 2020-05-16 [1] Bioconductor | |
| # sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2) | |
| # SummarizedExperiment * 1.18.2 2020-07-09 [1] Bioconductor | |
| # testthat * 2.3.2 2020-03-02 [1] CRAN (R 4.0.2) | |
| # tibble 3.0.3 2020-07-10 [1] CRAN (R 4.0.2) | |
| # tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2) | |
| # usethis * 1.6.3 2020-09-17 [1] CRAN (R 4.0.2) | |
| # vctrs 0.3.4 2020-08-29 [1] CRAN (R 4.0.2) | |
| # withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2) | |
| # XVector 0.28.0 2020-04-27 [1] Bioconductor | |
| # zlibbioc 1.34.0 2020-04-27 [1] Bioconductor | |
| # | |
| # [1] D:/R/R-4.0.2/library |
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