V-plot — vPlot • ATACseqQC

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

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.

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

Author

Jianhong Ou

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))