Count reads per cell overlapping a given set of regions
CountsInRegion(object, assay, regions, ...)
| object | A Seurat object |
|---|---|
| assay | Name of a chromatin assay in the object to use |
| regions | A GRanges object |
| ... | Additional arguments passed to |
Returns a numeric vector
# \donttest{ CountsInRegion( object = atac_small, assay = 'bins', regions = blacklist_hg19 )#> AAACGAAAGAGCGAAA-1 AAACGAAAGAGTTTGA-1 AAACGAAAGCGAGCTA-1 AAACGAAAGGCTTCGC-1 #> 0 0 2 9 #> AAACGAAAGTGCTGAG-1 AAACGAACAAGGGTAC-1 AAACGAAGTCAGGCTC-1 AAACGAAGTGCCCGAT-1 #> 0 3 1 2 #> AAACGAAGTTGTATCG-1 AAACGAATCAGTTGAC-1 AAACGAATCCTTACGC-1 AAACGAATCGTTTGAG-1 #> 0 0 1 0 #> AAACGAATCTGCCGAG-1 AAACTCGAGATGCGCA-1 AAACTCGAGCATGATA-1 AAACTCGAGCGCATTT-1 #> 0 0 0 0 #> AAACTCGAGTACTCTG-1 AAACTCGAGTCACGCC-1 AAACTCGAGTCTCTAG-1 AAACTCGCAAAGAGAG-1 #> 2 1 1 2 #> AAACTCGCAAGCGAAC-1 AAACTCGCACTCAGCG-1 AAACTCGCACTTGCGG-1 AAACTCGCAGCGTCGT-1 #> 0 0 0 1 #> AAACTCGCATCACAGT-1 AAACTCGCATGTGGGA-1 AAACTCGGTCAGAAGC-1 AAACTCGGTCATAGCT-1 #> 1 2 0 1 #> AAACTCGGTGGATTCT-1 AAACTCGGTTTGATCG-1 AAACTCGTCAGGTCTA-1 AAACTCGTCCACTAGA-1 #> 2 3 2 1 #> AAACTCGTCCCAATAG-1 AAACTCGTCGATGTAC-1 AAACTCGTCTGGCACG-1 AAACTCGTCTGGCGCA-1 #> 0 0 3 0 #> AAACTGCAGAATCAAC-1 AAACTGCAGAGTGGAA-1 AAACTGCAGCAAGGTC-1 AAACTGCAGCTCCATA-1 #> 1 0 1 2 #> AAACTGCAGTCTGTGT-1 AAACTGCCAACAAACA-1 AAACTGCCAAGAGATT-1 AAACTGCCAAGCCAGA-1 #> 2 1 0 1 #> AAACTGCCACTTGCGG-1 AAACTGCCATGTATCG-1 AAACTGCGTACTAGAA-1 AAACTGCGTCATAGCT-1 #> 0 16 1 1 #> AAACTGCGTCATGAGG-1 AAACTGCGTCGATTAC-1 AAACTGCGTGCATTCA-1 AAACTGCGTGCTGAAG-1 #> 0 1 1 0 #> AAACTGCGTTACCACA-1 AAACTGCTCATTCATC-1 AAACTGCTCCGTACGG-1 AAACTGCTCCTATCCG-1 #> 0 4 0 3 #> AAACTGCTCGTTCAGA-1 AAACTGCTCTGAGTAC-1 AAAGATGAGAAGGGCG-1 AAAGATGAGCGAGAAA-1 #> 1 0 2 0 #> AAAGATGAGGCTAAAT-1 AAAGATGAGTCCAGAG-1 AAAGATGAGTCGACCC-1 AAAGATGAGTTATGAG-1 #> 6 1 1 0 #> AAAGATGCAACCTCTC-1 AAAGATGCAAGGTCGA-1 AAAGATGCAAGTCTGT-1 AAAGATGCACGTTACA-1 #> 0 0 1 3 #> AAAGATGCAGCAACCC-1 AAAGATGCAGCACATT-1 AAAGATGCAGCGTCGT-1 AAAGATGCATGACTGT-1 #> 0 3 1 1 #> AAAGATGTCCACACCT-1 AAAGATGTCCTGAAAC-1 AAAGATGTCGCGGCAT-1 AAAGATGTCGCTAGTA-1 #> 4 1 0 0 #> AAAGATGTCGTCGCAG-1 AAAGATGTCTAGCAGT-1 AAAGGATAGAACCATA-1 AAAGGATAGAGAATTC-1 #> 3 1 0 0 #> AAAGGATAGAGGAACA-1 AAAGGATAGTCTGGGA-1 AAAGGATAGTGAGTTA-1 AAAGGATCAAGGGAGG-1 #> 0 0 0 2 #> AAAGGATCACCACCAG-1 AAAGGATCACGTTGTA-1 AAAGGATCAGATGGCA-1 AAAGGATCATGGAGGT-1 #> 0 1 2 13 #> AAAGGATGTCCCTTTG-1 AAAGGATGTCGTAATC-1 AAAGGATGTCTAAGAA-1 AAAGGATGTCTCAAAC-1 #> 1 1 2 0 #> AAAGGATGTCTTAGCA-1 AAAGGATGTGGACGAT-1 AAAGGATTCACTACCC-1 AAAGGATTCCAACCTC-1 #> 0 0 0 1 #> AAAGGATTCCGTCAAA-1 AAAGGATTCCTTACGC-1 AAAGGATTCTATGAGC-1 AAAGGATTCTGAACGT-1 #> 0 2 2 1# }