vPlot {ATACseqQC} | R Documentation

## V-plot

### Description

Aggregate ATAC-seq Fragment Midpoint vs. Length for a given motif generated over binding sites within the genome.

### Usage

    vPlot(
      bamfiles,
      index = bamfiles,
      pfm,
      genome,
      min.score = "95%",
      bindingSites,
      seqlev = paste0("chr", c(1:22, "X", "Y")),
      upstream = 200,
      downstream = 200,
      maxSiteNum = 1e+06,
      draw = TRUE,
      ...
    )

### Arguments

`bamfiles` | A vector of characters indicates the file names of bams. All the bamfiles will be pulled together.
`index` | The names of the index file of the 'BAM' file being processed; This is given without the '.bai' extension.
`pfm` | A Position frequency Matrix represented as a numeric matrix with row names A, C, G and T.
`genome` | An object of BSgenome.
`min.score` | The minimum score for counting a match. Can be given as a character string containing a percentage (e.g. "95 score or as a single number. See matchPWM.
`bindingSites` | A object of GRanges indicates candidate binding sites (eg. the output of fimo).
`seqlev` | A vector of characters indicates the sequence levels.
`upstream, downstream` | numeric(1) or integer(1). Upstream and downstream of the binding region for aggregate ATAC-seq footprint.
`maxSiteNum` | numeric(1). Maximal number of predicted binding sites. if predicted binding sites is more than this number, top maxSiteNum binding sites will be used.
`draw` | Plot or not. Default TRUE.
`...` | parameters could be used by smoothScatter

### Value

an invisible data.frame for plot.

### Author(s)

Jianhong Ou

### References

Jorja G. Henikoff, Jason A. Belsky, Kristina Krassovsky, David M. MacAlpine, and Steven Henikoff. Epigenome characterization at single base-pair resolution. PNAS 2011 108 (45) 18318-18323

### Examples

    bamfile <- system.file("extdata", "GL1.bam",
                           package="ATACseqQC")
    library(MotifDb)
    CTCF <- query(MotifDb, c("CTCF"))
    CTCF <- as.list(CTCF)
    library(BSgenome.Hsapiens.UCSC.hg19)
    vPlot(bamfile, pfm=CTCF[[1]],
         genome=Hsapiens,
         min.score="95%", seqlev="chr1",
         ylim=c(30, 250))

[Package ATACseqQC version 1.11.8 Index]