Read bedfile into GRanges

Read bedfile into GRanges

bed_to_granges(
  bedfile,
  genome,
  txdb = NULL,
  do_order = TRUE,
  plot = TRUE,
  verbose = TRUE
)

Arguments

bedfile	file path
genome	string: UCSC genome name (e.g. 'mm10')
txdb	NULL (default) or TxDb-class (used for gene annotation)
do_order	TRUE (default) or FALSE: order on seqnames and star?
plot	TRUE (default) or FALSE: plot karyogram?
verbose	TRUE (default) or FALSE

Value

GRanges-class

See also

char_to_granges, genes_to_granges

Examples

bedfile  <- system.file('extdata/SRF.bed', package = 'multicrispr')
bsgenome <- BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10
(gr <- bed_to_granges(bedfile, genome='mm10'))
#> 	Read SRF.bed into GRanges
#> 		1974 ranges on 21 chromosomes
#> GRanges object with 1974 ranges and 5 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
#>                            <integer>
#>     chr1:4712628-4712643:-   4712643
#>     chr1:5250212-5250227:-   5250227
#>     chr1:5250452-5250467:-   5250467
#>     chr1:5256193-5256208:-   5256208
#>     chr1:5985728-5985743:-   5985743
#>                        ...       ...
#>     chrY:6770312-6770327:+   6770327
#>   chrY:23130568-23130583:+  23130583
#>   chrY:42512400-42512415:-  42512415
#>   chrY:79048176-79048191:-  79048191
#>   chrY:89126494-89126509:-  89126509
#>   -------
#>   seqinfo: 66 sequences (1 circular) from mm10 genome