up_flank {multicrispr} | R Documentation

## Extend or Flank GRanges

### Description

Returns extensions, upstream flanks, or downstream flanks

### Usage

    up_flank(
      gr,
      start = -200,
      end = -1,
      strandaware = TRUE,
      bsgenome = NULL,
      verbose = FALSE,
      plot = FALSE,
      linetype_var = "set",
      ...
    )

    down_flank(
      gr,
      start = 1,
      end = 200,
      strandaware = TRUE,
      bsgenome = NULL,
      verbose = FALSE,
      plot = FALSE,
      linetype_var = "set",
      ...
    )

    extend(
      gr,
      start = -22,
      end = 22,
      strandaware = TRUE,
      bsgenome = NULL,
      verbose = FALSE,
      plot = FALSE,
      linetype_var = "set",
      ...
    )

### Arguments

`gr` | `GRanges-class`
`start` | number or vector (same length as gr): start definition, relative to gr start (up_flank, extend) or gr end (down_flank).
`end` | number or vector (same length as gr): end definition, relative to gr start (up_flank) or gr end (extend, down_flank).
`strandaware` | TRUE (default) or FALSE: consider strand information?
`bsgenome` | NULL (default) or `BSgenome-class`. Required to update gr$seq if present.
`verbose` | TRUE or FALSE (default)
`plot` | TRUE or FALSE (default)
`linetype_var` | string: gr var mapped to linetype
`...` | passed to `plot_intervals`

### Details

`up_flank` returns upstream flanks, in relation to start(gr). `down_flank` returns downstream flanks, in relation to end(gr). `extend` returns extensions, in relation to start(gr) and end(gr)

### Value

a `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 = bsgenome)
    gr %>% up_flank( -22,  -1, plot=TRUE)
    gr %>% up_flank( c(-10,-20,-30,-40),  -1, plot=TRUE)
    gr %>% up_flank( -22,  -1, plot=TRUE, strandaware=FALSE)

    gr %>% down_flank(+1, +22, plot=TRUE)
    gr %>% down_flank(+1, c(10, 20, 30, 40), plot=TRUE)
    gr %>% down_flank(+1, +22, plot=TRUE, strandaware=FALSE)

    gr %>% extend(   -10, +20, plot=TRUE)
    gr %>% extend(   -10, +20, plot=TRUE, strandaware=FALSE)

    # TFBS example
    #-------------
        bedfile <- system.file('extdata/SRF.bed', package='multicrispr')
        gr <- bed_to_granges(bedfile, genome = 'mm10')
        gr %>% extend(plot = TRUE)
        gr %>% up_flank(plot = TRUE)
        gr %>% down_flank(plot = TRUE)

[Package multicrispr version 1.2.0 Index]