Search for telomeres

Searches for telomeric repeats in the whole list of tandem repeats, or narrowing the search on the ends of sequence features.

Usage

telomeres(gr, motif = "TTAGGG", narrow = c("no", "ends"))

Arguments

gr

A GenomicRanges::GRanges object produced by the loadTantan function

motif

The telomeric sequence motif, at the end of the plus strand, like in TeloBase and the Telomerase Database.

narrow

Narrow the search on the ends.

Author

Charles Plessy

Examples

telomeres(exampleTantan)
#> GRanges object with 8 ranges and 5 metadata columns:
#>         seqnames          ranges strand |     score normTandem     nchar
#>            <Rle>       <IRanges>  <Rle> | <numeric>   <factor> <integer>
#>   [1] 1086a8205b           1-613      + | 102.66700     AACCCT         6
#>   [2] 1086a8205b   137225-137239      + |   2.50000     AACCCT         6
#>   [3] 1086a8205b 1005769-1005789      + |   3.50000     AACCCT         6
#>   [4] 1086a8205b 1284710-1284733      - |   4.00000     AACCCT         6
#>   [5] 1086a8205b 1286476-1286494      - |   3.16667     AACCCT         6
#>   [6] 1086a8205b 1288480-1288495      + |   2.66667     AACCCT         6
#>   [7] 1086a8205b 1505855-1505871      - |   2.83333     AACCCT         6
#>   [8] 1086a8205b 1663642-1663664      + |   3.83333     AACCCT         6
#>          rstart      rend
#>       <numeric> <numeric>
#>   [1]   2232853   2233465
#>   [2]   2096227   2096241
#>   [3]   1227677   1227697
#>   [4]    948733    948756
#>   [5]    946972    946990
#>   [6]    944971    944986
#>   [7]    727595    727611
#>   [8]    569802    569824
#>   -------
#>   seqinfo: 1 sequence from example genome
telomeres(exampleTantan, narrow="ends")
#> GRanges object with 1 range and 5 metadata columns:
#>         seqnames    ranges strand |     score normTandem     nchar    rstart
#>            <Rle> <IRanges>  <Rle> | <numeric>   <factor> <integer> <numeric>
#>   [1] 1086a8205b     1-613      + |   102.667     AACCCT         6   2232853
#>            rend
#>       <numeric>
#>   [1]   2233465
#>   -------
#>   seqinfo: 1 sequence from example genome