FractionCountsInRegion

Find the fraction of counts per cell that overlap a given set of genomic ranges

FractionCountsInRegion(object, assay, regions, sep = c("-", "-"), ...)

Arguments

object	A Seurat object
assay	Name of assay to use
regions	A GRanges object containing a set of genomic regions
sep	The separator used to separate genomic coordinate information in the assay feature names
...	Additional arguments passed to CountsInRegion

Value

Returns a numeric vector

Examples

FractionCountsInRegion(
  object = atac_small,
  assay = 'bins',
  regions = blacklist_hg19
)
#> AAACGAAAGAGCGAAA-1 AAACGAAAGAGTTTGA-1 AAACGAAAGCGAGCTA-1 AAACGAAAGGCTTCGC-1 
#>         0.00000000         0.00000000         0.15384615         0.05769231 
#> AAACGAAAGTGCTGAG-1 AAACGAACAAGGGTAC-1 AAACGAAGTCAGGCTC-1 AAACGAAGTGCCCGAT-1 
#>         0.00000000                NaN         0.33333333         0.22222222 
#> AAACGAAGTTGTATCG-1 AAACGAATCAGTTGAC-1 AAACGAATCCTTACGC-1 AAACGAATCGTTTGAG-1 
#>         0.00000000                NaN         1.00000000         0.00000000 
#> AAACGAATCTGCCGAG-1 AAACTCGAGATGCGCA-1 AAACTCGAGCATGATA-1 AAACTCGAGCGCATTT-1 
#>         0.00000000         0.00000000         0.00000000         0.00000000 
#> AAACTCGAGTACTCTG-1 AAACTCGAGTCACGCC-1 AAACTCGAGTCTCTAG-1 AAACTCGCAAAGAGAG-1 
#>         0.05882353         0.07692308         0.00000000         0.12500000 
#> AAACTCGCAAGCGAAC-1 AAACTCGCACTCAGCG-1 AAACTCGCACTTGCGG-1 AAACTCGCAGCGTCGT-1 
#>                NaN         0.00000000         0.00000000         0.10000000 
#> AAACTCGCATCACAGT-1 AAACTCGCATGTGGGA-1 AAACTCGGTCAGAAGC-1 AAACTCGGTCATAGCT-1 
#>         0.16666667         0.02222222         0.00000000         0.00000000 
#> AAACTCGGTGGATTCT-1 AAACTCGGTTTGATCG-1 AAACTCGTCAGGTCTA-1 AAACTCGTCCACTAGA-1 
#>         0.33333333         0.09375000         0.16666667         0.14285714 
#> AAACTCGTCCCAATAG-1 AAACTCGTCGATGTAC-1 AAACTCGTCTGGCACG-1 AAACTCGTCTGGCGCA-1 
#>         0.00000000         0.00000000         0.40000000         0.00000000 
#> AAACTGCAGAATCAAC-1 AAACTGCAGAGTGGAA-1 AAACTGCAGCAAGGTC-1 AAACTGCAGCTCCATA-1 
#>         0.06250000         0.00000000         0.50000000         0.13333333 
#> AAACTGCAGTCTGTGT-1 AAACTGCCAACAAACA-1 AAACTGCCAAGAGATT-1 AAACTGCCAAGCCAGA-1 
#>         1.00000000         0.20000000         0.00000000         0.50000000 
#> AAACTGCCACTTGCGG-1 AAACTGCCATGTATCG-1 AAACTGCGTACTAGAA-1 AAACTGCGTCATAGCT-1 
#>         0.00000000         0.26086957         0.33333333         0.20000000 
#> AAACTGCGTCATGAGG-1 AAACTGCGTCGATTAC-1 AAACTGCGTGCATTCA-1 AAACTGCGTGCTGAAG-1 
#>         0.00000000         0.00000000         0.07142857         0.00000000 
#> AAACTGCGTTACCACA-1 AAACTGCTCATTCATC-1 AAACTGCTCCGTACGG-1 AAACTGCTCCTATCCG-1 
#>         0.00000000         0.42857143                NaN         0.28571429 
#> AAACTGCTCGTTCAGA-1 AAACTGCTCTGAGTAC-1 AAAGATGAGAAGGGCG-1 AAAGATGAGCGAGAAA-1 
#>         0.25000000         0.00000000         0.14285714         0.00000000 
#> AAAGATGAGGCTAAAT-1 AAAGATGAGTCCAGAG-1 AAAGATGAGTCGACCC-1 AAAGATGAGTTATGAG-1 
#>         0.19047619         0.05882353         0.33333333         0.00000000 
#> AAAGATGCAACCTCTC-1 AAAGATGCAAGGTCGA-1 AAAGATGCAAGTCTGT-1 AAAGATGCACGTTACA-1 
#>         0.00000000         0.00000000         0.33333333         0.08333333 
#> AAAGATGCAGCAACCC-1 AAAGATGCAGCACATT-1 AAAGATGCAGCGTCGT-1 AAAGATGCATGACTGT-1 
#>         0.00000000         0.23076923         0.00000000         0.05882353 
#> AAAGATGTCCACACCT-1 AAAGATGTCCTGAAAC-1 AAAGATGTCGCGGCAT-1 AAAGATGTCGCTAGTA-1 
#>         0.20000000         0.09090909         0.00000000         0.00000000 
#> AAAGATGTCGTCGCAG-1 AAAGATGTCTAGCAGT-1 AAAGGATAGAACCATA-1 AAAGGATAGAGAATTC-1 
#>         0.03703704         0.05555556         0.00000000         0.00000000 
#> AAAGGATAGAGGAACA-1 AAAGGATAGTCTGGGA-1 AAAGGATAGTGAGTTA-1 AAAGGATCAAGGGAGG-1 
#>         0.00000000         0.00000000         0.00000000         0.13333333 
#> AAAGGATCACCACCAG-1 AAAGGATCACGTTGTA-1 AAAGGATCAGATGGCA-1 AAAGGATCATGGAGGT-1 
#>         0.00000000         0.20000000         0.08695652         0.60000000 
#> AAAGGATGTCCCTTTG-1 AAAGGATGTCGTAATC-1 AAAGGATGTCTAAGAA-1 AAAGGATGTCTCAAAC-1 
#>         0.25000000         0.16666667         0.07692308         0.00000000 
#> AAAGGATGTCTTAGCA-1 AAAGGATGTGGACGAT-1 AAAGGATTCACTACCC-1 AAAGGATTCCAACCTC-1 
#>         0.00000000         0.00000000         0.00000000         0.00000000 
#> AAAGGATTCCGTCAAA-1 AAAGGATTCCTTACGC-1 AAAGGATTCTATGAGC-1 AAAGGATTCTGAACGT-1 
#>         0.00000000         0.12500000         0.33333333         0.00000000