Add inverse strand

Add inverse strand

add_inverse_strand(gr, verbose = FALSE, plot = FALSE, ...)

Arguments

gr	GRanges-class
verbose	TRUE or FALSE (default)
plot	TRUE or FALSE (default)
...	plot_intervals arguments

Value

GRanges-class

Examples

# PE example
#-----------
    require(magrittr)
#> Lade nötiges Paket: 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)
    add_inverse_strand(gr, plot = TRUE)
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> Warning: Zeichenbreite unbekannt für das Zeichen 0x9
#> GRanges object with 8 ranges and 3 metadata columns:
#>          seqnames              ranges strand |  targetname targetstart
#>             <Rle>           <IRanges>  <Rle> | <character>   <integer>
#>   CFTR_f     chr7 117559593-117559595      + |        CFTR   117559593
#>   CFTR_r     chr7 117559593-117559595      - |        CFTR   117559593
#>    HBB_r    chr11             5227002      - |         HBB     5227002
#>    HBB_f    chr11             5227002      + |         HBB     5227002
#>   HEXA_r    chr15   72346580-72346583      - |        HEXA    72346580
#>   HEXA_f    chr15   72346580-72346583      + |        HEXA    72346580
#>   PRNP_f    chr20             4699600      + |        PRNP     4699600
#>   PRNP_r    chr20             4699600      - |        PRNP     4699600
#>          targetend
#>          <integer>
#>   CFTR_f 117559595
#>   CFTR_r 117559595
#>    HBB_r   5227002
#>    HBB_f   5227002
#>   HEXA_r  72346583
#>   HEXA_f  72346583
#>   PRNP_f   4699600
#>   PRNP_r   4699600
#>   -------
#>   seqinfo: 595 sequences (1 circular) from hg38 genome
# TFBS example
#-------------
    bedfile <- system.file('extdata/SRF.bed', package='multicrispr')
    gr <- bed_to_granges(bedfile, genome = 'mm10')
#> 	Read SRF.bed into GRanges
#> 
#> Attache Paket: 'BiocGenerics'
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, sd, var, xtabs
#> The following objects are masked from 'package:base':
#> 
#>     anyDuplicated, append, as.data.frame, basename, cbind, colnames,
#>     dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
#>     grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
#>     order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
#>     rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
#>     union, unique, unsplit, which, which.max, which.min
#> 
#> Attache Paket: 'S4Vectors'
#> The following object is masked from 'package:base':
#> 
#>     expand.grid
#> 
#> Attache Paket: 'IRanges'
#> The following object is masked from 'package:grDevices':
#> 
#>     windows
#> 
#> Attache Paket: 'Biostrings'
#> The following object is masked from 'package:base':
#> 
#>     strsplit
#> 		1974 ranges on 21 chromosomes
    add_inverse_strand(gr)
#> GRanges object with 3948 ranges and 5 metadata columns:
#>                              seqnames            ranges strand |         name
#>                                 <Rle>         <IRanges>  <Rle> |  <character>
#>     chr1:4712628-4712643:-_r     chr1   4712628-4712643      - | SRF_MA0083.3
#>     chr1:4712628-4712643:-_f     chr1   4712628-4712643      + | SRF_MA0083.3
#>     chr1:5250212-5250227:-_r     chr1   5250212-5250227      - | SRF_MA0083.3
#>     chr1:5250212-5250227:-_f     chr1   5250212-5250227      + | SRF_MA0083.3
#>     chr1:5250452-5250467:-_r     chr1   5250452-5250467      - | SRF_MA0083.3
#>                          ...      ...               ...    ... .          ...
#>   chrY:42512400-42512415:-_f     chrY 42512400-42512415      + | SRF_MA0083.3
#>   chrY:79048176-79048191:-_r     chrY 79048176-79048191      - | SRF_MA0083.3
#>   chrY:79048176-79048191:-_f     chrY 79048176-79048191      + | SRF_MA0083.3
#>   chrY:89126494-89126509:-_r     chrY 89126494-89126509      - | SRF_MA0083.3
#>   chrY:89126494-89126509:-_f     chrY 89126494-89126509      + | SRF_MA0083.3
#>                                  score               targetname targetstart
#>                              <numeric>              <character>   <integer>
#>     chr1:4712628-4712643:-_r  10.49542   chr1:4712628-4712643:-     4712628
#>     chr1:4712628-4712643:-_f  10.49542   chr1:4712628-4712643:-     4712628
#>     chr1:5250212-5250227:-_r   9.73780   chr1:5250212-5250227:-     5250212
#>     chr1:5250212-5250227:-_f   9.73780   chr1:5250212-5250227:-     5250212
#>     chr1:5250452-5250467:-_r   5.92033   chr1:5250452-5250467:-     5250452
#>                          ...       ...                      ...         ...
#>   chrY:42512400-42512415:-_f   6.59053 chrY:42512400-42512415:-    42512400
#>   chrY:79048176-79048191:-_r   9.73780 chrY:79048176-79048191:-    79048176
#>   chrY:79048176-79048191:-_f   9.73780 chrY:79048176-79048191:-    79048176
#>   chrY:89126494-89126509:-_r   4.54393 chrY:89126494-89126509:-    89126494
#>   chrY:89126494-89126509:-_f   4.54393 chrY:89126494-89126509:-    89126494
#>                              targetend
#>                              <integer>
#>     chr1:4712628-4712643:-_r   4712643
#>     chr1:4712628-4712643:-_f   4712643
#>     chr1:5250212-5250227:-_r   5250227
#>     chr1:5250212-5250227:-_f   5250227
#>     chr1:5250452-5250467:-_r   5250467
#>                          ...       ...
#>   chrY:42512400-42512415:-_f  42512415
#>   chrY:79048176-79048191:-_r  79048191
#>   chrY:79048176-79048191:-_f  79048191
#>   chrY:89126494-89126509:-_r  89126509
#>   chrY:89126494-89126509:-_f  89126509
#>   -------
#>   seqinfo: 66 sequences (1 circular) from mm10 genome