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

FractionCountsInRegion(object, regions, assay = NULL, ...)

Arguments

object

A Seurat object

regions

A GRanges object containing a set of genomic regions

assay

Name of assay to use

...

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 
#>        0.000000000        0.000000000        0.019801980        0.012838802 
#> AAACGAAAGTGCTGAG-1 AAACGAACAAGGGTAC-1 AAACGAAGTCAGGCTC-1 AAACGAAGTGCCCGAT-1 
#>        0.000000000        0.032608696        0.037037037        0.046511628 
#> AAACGAAGTTGTATCG-1 AAACGAATCAGTTGAC-1 AAACGAATCCTTACGC-1 AAACGAATCGTTTGAG-1 
#>        0.000000000        0.000000000        0.083333333        0.000000000 
#> AAACGAATCTGCCGAG-1 AAACTCGAGATGCGCA-1 AAACTCGAGCATGATA-1 AAACTCGAGCGCATTT-1 
#>        0.000000000        0.000000000        0.000000000        0.000000000 
#> AAACTCGAGTACTCTG-1 AAACTCGAGTCACGCC-1 AAACTCGAGTCTCTAG-1 AAACTCGCAAAGAGAG-1 
#>        0.022727273        0.024390244        0.033333333        0.018348624 
#> AAACTCGCAAGCGAAC-1 AAACTCGCACTCAGCG-1 AAACTCGCACTTGCGG-1 AAACTCGCAGCGTCGT-1 
#>        0.000000000        0.000000000        0.000000000        0.013888889 
#> AAACTCGCATCACAGT-1 AAACTCGCATGTGGGA-1 AAACTCGGTCAGAAGC-1 AAACTCGGTCATAGCT-1 
#>        0.043478261        0.006514658        0.000000000        0.023809524 
#> AAACTCGGTGGATTCT-1 AAACTCGGTTTGATCG-1 AAACTCGTCAGGTCTA-1 AAACTCGTCCACTAGA-1 
#>        0.052631579        0.016483516        0.016666667        0.025000000 
#> AAACTCGTCCCAATAG-1 AAACTCGTCGATGTAC-1 AAACTCGTCTGGCACG-1 AAACTCGTCTGGCGCA-1 
#>        0.000000000        0.000000000        0.093750000        0.000000000 
#> AAACTGCAGAATCAAC-1 AAACTGCAGAGTGGAA-1 AAACTGCAGCAAGGTC-1 AAACTGCAGCTCCATA-1 
#>        0.010101010        0.000000000        0.500000000        0.054054054 
#> AAACTGCAGTCTGTGT-1 AAACTGCCAACAAACA-1 AAACTGCCAAGAGATT-1 AAACTGCCAAGCCAGA-1 
#>        0.400000000        0.014925373        0.000000000        0.100000000 
#> AAACTGCCACTTGCGG-1 AAACTGCCATGTATCG-1 AAACTGCGTACTAGAA-1 AAACTGCGTCATAGCT-1 
#>        0.000000000        0.142857143        0.030303030        0.037037037 
#> AAACTGCGTCATGAGG-1 AAACTGCGTCGATTAC-1 AAACTGCGTGCATTCA-1 AAACTGCGTGCTGAAG-1 
#>        0.000000000        0.021739130        0.010989011        0.000000000 
#> AAACTGCGTTACCACA-1 AAACTGCTCATTCATC-1 AAACTGCTCCGTACGG-1 AAACTGCTCCTATCCG-1 
#>        0.000000000        0.095238095        0.000000000        0.075000000 
#> AAACTGCTCGTTCAGA-1 AAACTGCTCTGAGTAC-1 AAAGATGAGAAGGGCG-1 AAAGATGAGCGAGAAA-1 
#>        0.041666667        0.000000000        0.042553191        0.000000000 
#> AAAGATGAGGCTAAAT-1 AAAGATGAGTCCAGAG-1 AAAGATGAGTCGACCC-1 AAAGATGAGTTATGAG-1 
#>        0.051724138        0.007692308        0.041666667        0.000000000 
#> AAAGATGCAACCTCTC-1 AAAGATGCAAGGTCGA-1 AAAGATGCAAGTCTGT-1 AAAGATGCACGTTACA-1 
#>        0.000000000        0.000000000        0.045454545        0.024793388 
#> AAAGATGCAGCAACCC-1 AAAGATGCAGCACATT-1 AAAGATGCAGCGTCGT-1 AAAGATGCATGACTGT-1 
#>        0.000000000        0.044117647        0.013333333        0.012048193 
#> AAAGATGTCCACACCT-1 AAAGATGTCCTGAAAC-1 AAAGATGTCGCGGCAT-1 AAAGATGTCGCTAGTA-1 
#>        0.063492063        0.015873016        0.000000000        0.000000000 
#> AAAGATGTCGTCGCAG-1 AAAGATGTCTAGCAGT-1 AAAGGATAGAACCATA-1 AAAGGATAGAGAATTC-1 
#>        0.015151515        0.008695652        0.000000000        0.000000000 
#> AAAGGATAGAGGAACA-1 AAAGGATAGTCTGGGA-1 AAAGGATAGTGAGTTA-1 AAAGGATCAAGGGAGG-1 
#>        0.000000000        0.000000000        0.000000000        0.021276596 
#> AAAGGATCACCACCAG-1 AAAGGATCACGTTGTA-1 AAAGGATCAGATGGCA-1 AAAGGATCATGGAGGT-1 
#>        0.000000000        0.035714286        0.017094017        0.302325581 
#> AAAGGATGTCCCTTTG-1 AAAGGATGTCGTAATC-1 AAAGGATGTCTAAGAA-1 AAAGGATGTCTCAAAC-1 
#>        0.038461538        0.066666667        0.021978022        0.000000000 
#> AAAGGATGTCTTAGCA-1 AAAGGATGTGGACGAT-1 AAAGGATTCACTACCC-1 AAAGGATTCCAACCTC-1 
#>        0.000000000        0.000000000        0.000000000        0.043478261 
#> AAAGGATTCCGTCAAA-1 AAAGGATTCCTTACGC-1 AAAGGATTCTATGAGC-1 AAAGGATTCTGAACGT-1 
#>        0.000000000        0.014814815        0.039215686        0.008620690