Extract cell names containing reads mapped within a given genomic region
GetCellsInRegion(tabix, region, sep = c("-", "-"), cells = NULL)
| tabix | Tabix object |
|---|---|
| region | A string giving the region to extract from the fragments file |
| sep | Vector of separators to use for genomic string. First element is used to separate chromosome and coordinates, second separator is used to separate start and end coordinates. |
| cells | Vector of cells to include in output. If NULL, include all cells |
Returns a list
fpath <- system.file("extdata", "fragments.tsv.gz", package="Signac") GetCellsInRegion(tabix = fpath, region = "chr1-10245-762629")#> $cells #> [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" #> #> $region #> [1] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [4] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [7] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [10] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [13] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [16] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [19] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [22] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [25] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [28] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [31] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [34] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [37] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [40] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [43] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [46] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [49] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [52] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [55] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [58] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [61] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [64] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [67] "chr1-10245-762629" "chr1-10245-762629" "chr1-10245-762629" #> [70] "chr1-10245-762629" #>