Add sequence to GRanges

Add sequence to GRanges

add_seq(gr, bsgenome, verbose = FALSE, as.character = TRUE)

Arguments

gr	GRanges-class
bsgenome	BSgenome-class
verbose	TRUE or FALSE (default)
as.character	TRUE (default) or FALSE

Value

GRanges-class

Examples

# PE example
#-----------
    require(magrittr)
    bsgenome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
    gr <- char_to_granges(c(PRNP = 'chr20:4699600:+',             # snp
                            HBB  = 'chr11:5227002:-',             # snp
                            HEXA = 'chr15:72346580-72346583:-',   # del
                            CFTR = 'chr7:117559593-117559595:+'), # ins
                          bsgenome)
   (gr %<>% add_seq(bsgenome))
#> GRanges object with 4 ranges and 4 metadata columns:
#>        seqnames              ranges strand |  targetname targetstart targetend
#>           <Rle>           <IRanges>  <Rle> | <character>   <integer> <integer>
#>   PRNP    chr20             4699600      + |        PRNP     4699600   4699600
#>    HBB    chr11             5227002      - |         HBB     5227002   5227002
#>   HEXA    chr15   72346580-72346583      - |        HEXA    72346580  72346583
#>   CFTR     chr7 117559593-117559595      + |        CFTR   117559593 117559595
#>                seq
#>        <character>
#>   PRNP           G
#>    HBB           A
#>   HEXA        TATC
#>   CFTR         TTT
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome

# TFBS example
#-------------
    bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
    bedfile  <- system.file('extdata/SRF.bed', package='multicrispr')
    gr <- bed_to_granges(bedfile, 'mm10')
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
    (gr %<>% add_seq(bsgenome))
#> GRanges object with 1974 ranges and 6 metadata columns:
#>                            seqnames            ranges strand |         name
#>                               <Rle>         <IRanges>  <Rle> |  <character>
#>     chr1:4712628-4712643:-     chr1   4712628-4712643      - | SRF_MA0083.3
#>     chr1:5250212-5250227:-     chr1   5250212-5250227      - | SRF_MA0083.3
#>     chr1:5250452-5250467:-     chr1   5250452-5250467      - | SRF_MA0083.3
#>     chr1:5256193-5256208:-     chr1   5256193-5256208      - | SRF_MA0083.3
#>     chr1:5985728-5985743:-     chr1   5985728-5985743      - | SRF_MA0083.3
#>                        ...      ...               ...    ... .          ...
#>     chrY:6770312-6770327:+     chrY   6770312-6770327      + | SRF_MA0083.3
#>   chrY:23130568-23130583:+     chrY 23130568-23130583      + | SRF_MA0083.3
#>   chrY:42512400-42512415:-     chrY 42512400-42512415      - | SRF_MA0083.3
#>   chrY:79048176-79048191:-     chrY 79048176-79048191      - | SRF_MA0083.3
#>   chrY:89126494-89126509:-     chrY 89126494-89126509      - | SRF_MA0083.3
#>                                score               targetname targetstart
#>                            <numeric>              <character>   <integer>
#>     chr1:4712628-4712643:-  10.49542   chr1:4712628-4712643:-     4712628
#>     chr1:5250212-5250227:-   9.73780   chr1:5250212-5250227:-     5250212
#>     chr1:5250452-5250467:-   5.92033   chr1:5250452-5250467:-     5250452
#>     chr1:5256193-5256208:-   9.73780   chr1:5256193-5256208:-     5256193
#>     chr1:5985728-5985743:-   9.44821   chr1:5985728-5985743:-     5985728
#>                        ...       ...                      ...         ...
#>     chrY:6770312-6770327:+   9.73780   chrY:6770312-6770327:+     6770312
#>   chrY:23130568-23130583:+   9.73780 chrY:23130568-23130583:+    23130568
#>   chrY:42512400-42512415:-   6.59053 chrY:42512400-42512415:-    42512400
#>   chrY:79048176-79048191:-   9.73780 chrY:79048176-79048191:-    79048176
#>   chrY:89126494-89126509:-   4.54393 chrY:89126494-89126509:-    89126494
#>                            targetend              seq
#>                            <integer>      <character>
#>     chr1:4712628-4712643:-   4712643 AGACAATATAAGGGCA
#>     chr1:5250212-5250227:-   5250227 AGACAATATAAGGACA
#>     chr1:5250452-5250467:-   5250467 TGACAATATTTGGAAT
#>     chr1:5256193-5256208:-   5256208 AGACAATATAAGGACA
#>     chr1:5985728-5985743:-   5985743 CCACCAAATATGGGCT
#>                        ...       ...              ...
#>     chrY:6770312-6770327:+   6770327 AGACAATATAAGGACA
#>   chrY:23130568-23130583:+  23130583 AGACAATATAAGGACA
#>   chrY:42512400-42512415:-  42512415 TGGCCAAATATGTGGA
#>   chrY:79048176-79048191:-  79048191 AGACAATATAAGGACA
#>   chrY:89126494-89126509:-  89126509 TGCCCATACTAGGGAG
#>   -------
#>   seqinfo: 66 sequences (1 circular) from mm10 genome