Get cells in a region

Source: R/utilities.R

Extract cell names containing reads mapped within a given genomic region

GetCellsInRegion(tabix, region, cells = NULL)

Arguments

tabix

Tabix object
region

A string giving the region to extract from the fragments file
cells

Vector of cells to include in output. If NULL, include all cells

Value

Returns a list

Examples

fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac")
GetCellsInRegion(tabix = fpath, region = "chr1-10245-762629")

#> $`chr1:10245-762629`
#>  [1] "AAAGATGAGGCTAAAT-1" "AAACTCGTCTGGCACG-1" "AAACTCGTCTGGCACG-1"
#>  [4] "AAACTGCAGTCTGTGT-1" "AAACTGCTCCTATCCG-1" "AAAGGATTCCTTACGC-1"
#>  [7] "AAAGATGAGAAGGGCG-1" "AAACGAAGTGCCCGAT-1" "AAACTGCAGTCTGTGT-1"
#> [10] "AAACGAAAGGCTTCGC-1" "AAACTCGCAGCGTCGT-1" "AAACGAAGTGCCCGAT-1"
#> [13] "AAACGAATCCTTACGC-1" "AAAGGATCATGGAGGT-1" "AAACTGCTCCTATCCG-1"
#> [16] "AAAGATGCACGTTACA-1" "AAAGATGTCCACACCT-1" "AAACGAAAGGCTTCGC-1"
#> [19] "AAACTGCAGAATCAAC-1" "AAACTCGGTTTGATCG-1" "AAAGATGCAAGTCTGT-1"
#> [22] "AAACTCGTCAGGTCTA-1" "AAACGAAAGGCTTCGC-1" "AAACTGCGTGCATTCA-1"
#> [25] "AAACTGCTCCTATCCG-1" "AAACTGCCATGTATCG-1" "AAAGGATTCCTTACGC-1"
#> [28] "AAACTGCCAAGCCAGA-1" "AAACTCGAGTACTCTG-1" "AAACTGCTCGTTCAGA-1"
#> [31] "AAAGGATGTCGTAATC-1" "AAAGGATTCTATGAGC-1" "AAACGAAGTCAGGCTC-1"
#> [34] "AAACTGCAGCTCCATA-1" "AAAGATGAGTCCAGAG-1" "AAAGATGTCCACACCT-1"
#> [37] "AAAGATGTCCACACCT-1" "AAACTGCTCATTCATC-1" "AAACGAAAGCGAGCTA-1"
#> [40] "AAACTCGGTGGATTCT-1" "AAACGAAAGGCTTCGC-1" "AAACTCGTCTGGCACG-1"
#> [43] "AAAGATGTCTAGCAGT-1" "AAAGGATCAGATGGCA-1" "AAACTGCGTACTAGAA-1"
#> [46] "AAACGAAAGGCTTCGC-1" "AAAGATGAGGCTAAAT-1" "AAAGATGAGGCTAAAT-1"
#> [49] "AAACTCGAGTACTCTG-1" "AAAGATGTCCTGAAAC-1" "AAAGGATCAAGGGAGG-1"
#> [52] "AAAGATGCAGCACATT-1" "AAACTCGGTTTGATCG-1" "AAACTCGGTGGATTCT-1"
#> [55] "AAACTCGCAAAGAGAG-1" "AAAGATGAGTCGACCC-1" "AAACTCGCATCACAGT-1"
#> [58] "AAAGGATTCTATGAGC-1" "AAAGGATGTCCCTTTG-1" "AAACTGCCAACAAACA-1"
#> [61] "AAAGATGCATGACTGT-1" "AAAGATGAGAAGGGCG-1" "AAACTCGTCCACTAGA-1"
#> [64] "AAAGATGCACGTTACA-1" "AAAGATGCAGCGTCGT-1" "AAACGAAAGGCTTCGC-1"
#> [67] "AAAGGATGTCTAAGAA-1" "AAACGAAGTTGTATCG-1" "AAAGGATAGAACCATA-1"
#> [70] "AAACTCGCATGTGGGA-1"
#>