## Warning in sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x =
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## Warning in sparseMatrix(i = indices[] + 1, p = indptr[], x = as.numeric(x =
## counts[]), : 'giveCsparse' has been deprecated; setting 'repr = "T"' for you## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
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## ('-')
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## ('-')
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## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')
## Warning: Feature names cannot have underscores ('_'), replacing with dashes
## ('-')## sdata.SScILD_S19584_Tripleminus_AAACCTGAGAAAGTGG-1
## MT-TF 0
## MT-RNR1 2
## MT-TV 2
## MT-RNR2 4
## MT-TL1 1
## MT-ND1 4
## MT-TI 0
## MT-TQ 0
## MT-TM 0
## MT-ND2 2
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGCTCCCAG-1
## MT-TF 0
## MT-RNR1 2
## MT-TV 7
## MT-RNR2 2
## MT-TL1 0
## MT-ND1 3
## MT-TI 0
## MT-TQ 0
## MT-TM 1
## MT-ND2 5
## orig.ident
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGAAAGTGG-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGCTCCCAG-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGGATGTAT-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGTTAGGTA-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGAAT-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGTCT-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACGGTGTC-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTCGACG-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTTGGAT-1 SScILD_S19584_Tripleminus
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAGTGAGTG-1 SScILD_S19584_Tripleminus
## nCount_RNA nFeature_RNA
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGAAAGTGG-1 1335 572
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGCTCCCAG-1 759 479
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGGATGTAT-1 3732 1464
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGTTAGGTA-1 783 473
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGAAT-1 7493 2080
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGTCT-1 9782 2262
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACGGTGTC-1 7133 2678
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTCGACG-1 4650 1549
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTTGGAT-1 582 241
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAGTGAGTG-1 12683 2507
## disease patient type
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGAAAGTGG-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGCTCCCAG-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGGATGTAT-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGAGTTAGGTA-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGAAT-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAATGGTCT-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACGGTGTC-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTCGACG-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCACTTGGAT-1 SSc-ILD S19584 Triple-
## sdata.SScILD_S19584_Tripleminus_AAACCTGCAGTGAGTG-1 SSc-ILD S19584 Triple-## [1] "MT-TF" "MT-RNR1" "MT-TV" "MT-RNR2" "MT-TL1" "MT-ND1" "MT-TI"
## [8] "MT-TQ" "MT-TM" "MT-ND2"## [1] "RPL23AP53" "RPL14P3" "RPL23AP83" "RPL30P4" "RPS2P28" "RPL12P47"
## [7] "RPL26P30" "RPL6P8" "RPL5P2" "RPLP0P6"calculate the percentage of mitocondrial and ribosomal genes per cell and plot some of the QC-features as violin plots.