Last updated: 2022-09-14
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Knit directory: chromap_vs_cellranger_scATAC_exploration_10x/
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| Rmd | 10fdcb0 | jeremymsimon | 2022-09-14 | Initial commit |
library(tidyverse)── Attaching packages ─────────────────────────────────────── tidyverse 1.3.1 ──✔ ggplot2 3.3.6 ✔ purrr 0.3.4
✔ tibble 3.1.8 ✔ dplyr 1.0.9
✔ tidyr 1.2.0 ✔ stringr 1.4.0
✔ readr 2.1.2 ✔ forcats 0.5.1── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag() masks stats::lag()library(GenomicRanges)Loading required package: stats4Loading required package: BiocGenerics
Attaching package: 'BiocGenerics'The following objects are masked from 'package:dplyr':
combine, intersect, setdiff, unionThe following objects are masked from 'package:stats':
IQR, mad, sd, var, xtabsThe following objects are masked from 'package:base':
anyDuplicated, append, as.data.frame, basename, cbind, colnames,
dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unsplit, which.max, which.minLoading required package: S4Vectors
Attaching package: 'S4Vectors'The following objects are masked from 'package:dplyr':
first, renameThe following object is masked from 'package:tidyr':
expandThe following objects are masked from 'package:base':
expand.grid, I, unnameLoading required package: IRanges
Attaching package: 'IRanges'The following objects are masked from 'package:dplyr':
collapse, desc, sliceThe following object is masked from 'package:purrr':
reduceLoading required package: GenomeInfoDblibrary(Seurat)Attaching SeuratObjectlibrary(Signac)
library(EnsDb.Hsapiens.v86)Loading required package: ensembldbLoading required package: GenomicFeaturesLoading required package: AnnotationDbiLoading required package: BiobaseWelcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'AnnotationDbi'The following object is masked from 'package:dplyr':
selectLoading required package: AnnotationFilter
Attaching package: 'ensembldb'The following object is masked from 'package:dplyr':
filterThe following object is masked from 'package:stats':
filterannotations <- GetGRangesFromEnsDb(ensdb = EnsDb.Hsapiens.v86)Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Warning in .Seqinfo.mergexy(x, y): The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)seqlevelsStyle(annotations) <- 'UCSC'
genome(annotations) <- "hg38"p <- as.data.frame(read.table("cCRE_hg38_10x_HGMM_PBMC_chromap_fragments_MACS_q01_unionPeaks_merge100.bed",header=F,sep="\t"))
colnames(p) <- c("chr","start","stop")
peaks <- makeGRangesFromDataFrame(p)Computing hashExtracting reads overlapping genomic regionsWarning: Feature names cannot have underscores ('_'), replacing with dashes
('-')Warning: Keys should be one or more alphanumeric characters followed by an
underscore, setting key from peaks to peaks_HGMM_10x_path <- "10x_HGMM_chromap_fragments.tsv.gz"
HGMM_10x_cells <- read_tsv(HGMM_10x_path,col_names=c("chr","start","stop","cell","support"),col_types=c("-","-","-","-","c"),col_select="cell") %>%
pull(cell) %>%
unique()
names(x = HGMM_10x_cells) <- paste0("HGMM_", HGMM_10x_cells)
HGMM_10x_frags <- CreateFragmentObject(path = HGMM_10x_path, cells = HGMM_10x_cells, max.lines=NULL)
HGMM_10x_mat <- FeatureMatrix(
fragments = HGMM_10x_frags,
features = peaks,
process_n = 20000,
sep = c("-", "-"),
verbose = TRUE
)
HGMM_10x_assay <- CreateChromatinAssay(HGMM_10x_mat, fragments = HGMM_10x_frags, genome = 'hg38', min.features = 500)
HGMM_10x_seurat <- CreateSeuratObject(HGMM_10x_assay, assay = "peaks")
HGMM_10x_seurat$Sample <- "HGMM"Computing hashExtracting reads overlapping genomic regionsWarning: Feature names cannot have underscores ('_'), replacing with dashes
('-')Warning: Keys should be one or more alphanumeric characters followed by an
underscore, setting key from peaks to peaks_PBMC_10x_path <- "10x_PBMC_chromap_fragments.tsv.gz"
PBMC_10x_cells <- read_tsv(PBMC_10x_path,col_names=c("chr","start","stop","cell","support"),col_types=c("-","-","-","-","c"),col_select="cell") %>%
pull(cell) %>%
unique()
names(x = PBMC_10x_cells) <- paste0("PBMC_", PBMC_10x_cells)
PBMC_10x_frags <- CreateFragmentObject(path = PBMC_10x_path, cells = PBMC_10x_cells, max.lines=NULL)
PBMC_10x_mat <- FeatureMatrix(
fragments = PBMC_10x_frags,
features = peaks,
process_n = 20000,
sep = c("-", "-"),
verbose = TRUE
)
PBMC_10x_assay <- CreateChromatinAssay(PBMC_10x_mat, fragments = PBMC_10x_frags, genome = 'hg38', min.features = 500)
PBMC_10x_seurat <- CreateSeuratObject(PBMC_10x_assay, assay = "peaks")
PBMC_10x_seurat$Sample <- "PBMC"save.image("cCRE_hg38_10x_HGMM_PBMC_chromap_fragments_MACS_q01_unionPeaks_merge100_seurat_090222.RData")
sessionInfo()R version 4.1.0 (2021-05-18)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.5 (Ootpa)
Matrix products: default
BLAS/LAPACK: /nas/longleaf/rhel8/apps/r/4.1.0/lib/libopenblas_haswellp-r0.3.5.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] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] EnsDb.Hsapiens.v86_2.99.0 ensembldb_2.18.3
[3] AnnotationFilter_1.18.0 GenomicFeatures_1.46.5
[5] AnnotationDbi_1.56.2 Biobase_2.54.0
[7] Signac_1.7.0.9003 SeuratObject_4.0.4
[9] Seurat_4.1.0 GenomicRanges_1.46.1
[11] GenomeInfoDb_1.30.1 IRanges_2.28.0
[13] S4Vectors_0.32.4 BiocGenerics_0.40.0
[15] forcats_0.5.1 stringr_1.4.0
[17] dplyr_1.0.9 purrr_0.3.4
[19] readr_2.1.2 tidyr_1.2.0
[21] tibble_3.1.8 ggplot2_3.3.6
[23] tidyverse_1.3.1 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] utf8_1.2.2 reticulate_1.25
[3] tidyselect_1.1.2 RSQLite_2.2.10
[5] htmlwidgets_1.5.4 grid_4.1.0
[7] BiocParallel_1.28.3 Rtsne_0.15
[9] munsell_0.5.0 codetools_0.2-18
[11] ica_1.0-2 future_1.24.0
[13] miniUI_0.1.1.1 withr_2.5.0
[15] spatstat.random_2.1-0 colorspace_2.0-3
[17] filelock_1.0.2 knitr_1.37
[19] rstudioapi_0.13 ROCR_1.0-11
[21] tensor_1.5 listenv_0.8.0
[23] MatrixGenerics_1.6.0 git2r_0.30.1
[25] GenomeInfoDbData_1.2.7 polyclip_1.10-0
[27] bit64_4.0.5 rprojroot_2.0.2
[29] parallelly_1.30.0 vctrs_0.4.1
[31] generics_0.1.2 xfun_0.30
[33] biovizBase_1.42.0 BiocFileCache_2.2.1
[35] R6_2.5.1 DelayedArray_0.20.0
[37] bitops_1.0-7 spatstat.utils_2.3-0
[39] cachem_1.0.6 assertthat_0.2.1
[41] vroom_1.5.7 BiocIO_1.4.0
[43] promises_1.2.0.1 scales_1.2.0
[45] nnet_7.3-17 gtable_0.3.0
[47] globals_0.14.0 processx_3.5.2
[49] goftest_1.2-3 rlang_1.0.4
[51] RcppRoll_0.3.0 splines_4.1.0
[53] rtracklayer_1.54.0 lazyeval_0.2.2
[55] dichromat_2.0-0 checkmate_2.0.0
[57] spatstat.geom_2.3-2 broom_1.0.0
[59] yaml_2.3.5 reshape2_1.4.4
[61] abind_1.4-5 modelr_0.1.8
[63] backports_1.4.1 httpuv_1.6.5
[65] Hmisc_4.6-0 tools_4.1.0
[67] ellipsis_0.3.2 spatstat.core_2.4-0
[69] jquerylib_0.1.4 RColorBrewer_1.1-3
[71] ggridges_0.5.3 Rcpp_1.0.8.3
[73] plyr_1.8.7 base64enc_0.1-3
[75] progress_1.2.2 zlibbioc_1.40.0
[77] RCurl_1.98-1.6 prettyunits_1.1.1
[79] ps_1.6.0 rpart_4.1.16
[81] deldir_1.0-6 pbapply_1.5-0
[83] cowplot_1.1.1 zoo_1.8-9
[85] SummarizedExperiment_1.24.0 haven_2.4.3
[87] ggrepel_0.9.1 cluster_2.1.2
[89] fs_1.5.2 magrittr_2.0.2
[91] data.table_1.14.2 scattermore_0.8
[93] lmtest_0.9-40 reprex_2.0.1
[95] RANN_2.6.1 whisker_0.4
[97] ProtGenerics_1.26.0 fitdistrplus_1.1-6
[99] matrixStats_0.62.0 hms_1.1.1
[101] patchwork_1.1.1 mime_0.12
[103] evaluate_0.15 xtable_1.8-4
[105] XML_3.99-0.9 jpeg_0.1-9
[107] readxl_1.3.1 gridExtra_2.3
[109] biomaRt_2.50.3 compiler_4.1.0
[111] KernSmooth_2.23-20 crayon_1.5.1
[113] htmltools_0.5.2 mgcv_1.8-40
[115] later_1.3.0 tzdb_0.2.0
[117] Formula_1.2-4 lubridate_1.8.0
[119] DBI_1.1.2 dbplyr_2.1.1
[121] rappdirs_0.3.3 MASS_7.3-55
[123] Matrix_1.4-0 cli_3.3.0
[125] parallel_4.1.0 igraph_1.3.3
[127] pkgconfig_2.0.3 GenomicAlignments_1.30.0
[129] getPass_0.2-2 foreign_0.8-82
[131] plotly_4.10.0 spatstat.sparse_2.1-0
[133] xml2_1.3.3 bslib_0.3.1
[135] XVector_0.34.0 rvest_1.0.2
[137] VariantAnnotation_1.40.0 callr_3.7.0
[139] digest_0.6.29 sctransform_0.3.3
[141] RcppAnnoy_0.0.19 spatstat.data_2.1-2
[143] Biostrings_2.62.0 rmarkdown_2.12
[145] cellranger_1.1.0 leiden_0.3.9
[147] fastmatch_1.1-3 htmlTable_2.4.0
[149] uwot_0.1.11 restfulr_0.0.13
[151] curl_4.3.2 shiny_1.7.1
[153] Rsamtools_2.10.0 rjson_0.2.21
[155] lifecycle_1.0.1 nlme_3.1-155
[157] jsonlite_1.8.0 BSgenome_1.62.0
[159] viridisLite_0.4.0 fansi_1.0.3
[161] pillar_1.7.0 lattice_0.20-45
[163] KEGGREST_1.34.0 fastmap_1.1.0
[165] httr_1.4.2 survival_3.2-13
[167] glue_1.6.2 png_0.1-7
[169] bit_4.0.4 stringi_1.7.6
[171] sass_0.4.0 blob_1.2.2
[173] latticeExtra_0.6-29 memoise_2.0.1
[175] irlba_2.3.5 future.apply_1.8.1