Wrap Seurat Multiomics clustering

This function allows you to perform standard sc-multiome clustering

Multi_Wrapper(
 
    path = "/lab/solexa_weissman/cweng/Projects/MitoTracing_Velocity/SecondaryAnalysis/Donor01_CD34_1_Multiomekit/CellRanger/Donor01_CD34_1/outs",
  atacmin = 1000,
  umimin = 1000,
  CellID = NULL
)

Arguments

path

this should be the path to the cell-ranger results XX/outs

atacmin

minimum atac fragment for each cell, default is 1000

umimin

minimum rna umi for each cell, default is 1000

cellID

to be used for input(useful for re-clustering), default is NULL which will use the info from path/per_barcode_metrics.csv

Value

this returns seurat object with both RNA and ATAC

Examples

Multi_Wrapper(path="XX/CellRanger/Donor01_BMMC_1/outs/")
#> Loading required package: Signac
#> Loading required package: EnsDb.Hsapiens.v86
#> Loading required package: ensembldb
#> Loading required package: BiocGenerics
#> 
#> Attaching package: ‘BiocGenerics’
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#>     as.data.frame, basename, cbind, colnames, dirname, do.call,
#>     duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
#>     lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
#>     pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
#>     tapply, union, unique, unsplit, which.max, which.min
#> Loading required package: GenomicRanges
#> Loading required package: stats4
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#> Attaching package: ‘S4Vectors’
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#>     I, expand.grid, unname
#> Loading required package: IRanges
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#> Attaching package: ‘IRanges’
#> The following object is masked from ‘package:sp’:
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#>     %over%
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#> Welcome to Bioconductor
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#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> Loading required package: AnnotationFilter
#> 
#> Attaching package: 'ensembldb'
#> The following object is masked from 'package:stats':
#> 
#>     filter
#> Loading required package: dplyr
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#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:ensembldb':
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#>     filter, select
#> The following object is masked from 'package:AnnotationDbi':
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#> The following object is masked from 'package:Biobase':
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#> The following objects are masked from 'package:GenomicRanges':
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#> The following object is masked from 'package:GenomeInfoDb':
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#>     intersect
#> The following objects are masked from 'package:IRanges':
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#>     collapse, desc, intersect, setdiff, slice, union
#> The following objects are masked from 'package:S4Vectors':
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#>     first, intersect, rename, setdiff, setequal, union
#> The following objects are masked from 'package:BiocGenerics':
#> 
#>     combine, intersect, setdiff, union
#> The following objects are masked from 'package:stats':
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#>     filter, lag
#> The following objects are masked from 'package:base':
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#>     intersect, setdiff, setequal, union
#> Loading required package: ggplot2
#> Error in Read10X_h5(paste(path, "/raw_feature_bc_matrix.h5", sep = "")): File not found