Create ChIP Peak Binding Profile.

Create ChIP Peak Binding Profile.

PeakProfile(
  peak.df,
  species = c("Human", "Mouse", "Rat", "Fly", "Arabidopsis", "Yeast", "Zebrafish",
    "Worm", "Bovine", "Pig", "Chicken", "Rhesus", "Canine", "Xenopus", "Anopheles",
    "Chimp", "E coli strain Sakai", "Myxococcus xanthus DK 1622"),
  gtf.file = NULL,
  weight.col = NULL,
  up.dist = 3000,
  down.dist = 3000,
  color = "red",
  conf = 0.95,
  up.rel = 0.2,
  down.rel = 0.2,
  by = c("gene", "transcript", "exon", "intron", "3UTR", "5UTR"),
  region.type = c("start_site", "end_site", "body"),
  nbin = NULL
)

Arguments

peak.df

Dataframe contains all consensus peaks.
species

Species used, chosen from "Human","Mouse","Rat","Fly","Arabidopsis", "Yeast","Zebrafish","Worm","Bovine","Pig","Chicken","Rhesus", "Canine","Xenopus","Anopheles","Chimp","E coli strain Sakai","Myxococcus xanthus DK 1622". Default: "Human".
gtf.file

GTF file used to create TxDb object. Useful when specie you used is not available in species. Default: NULL.
weight.col

The column name of weight. Parameter of peakHeatmap, plotAvgProf2, plotPeakProf2. Default: NULL.
up.dist

The upstream distance from the TSS. Default: 3000bp.
down.dist

The downstream distance from the TSS. Default: 3000bp.
color

The color used for heatmap. Parameter of peakHeatmap. Default: red.
conf

The confidence interval. Parameter of plotAvgProf2, plotPeakProf2. Default: 0.95.
up.rel

The percentage of total length of body regions used as upstream distance from the TSS. Parameter of plotPeakProf2. When set NULL, use up.dist. Default: 0.2.
down.rel

The percentage of total length of body regions used as downstream distance from the TSS. Parameter of plotPeakProf2. When set NULL, use down.dist. Default: 0.2.
by

One of 'gene', 'transcript', 'exon', 'intron' , '3UTR' , '5UTR'. Parameter of plotPeakProf2. Default: 'gene'.
region.type

One of "start_site", "end_site", "body". Parameter of plotPeakProf2. Default: 'start_site'.
nbin

The amount of nbines. Parameter of plotPeakProf2. Default: NULL.

Value

List contains all profile plots.

Examples

library(DEbPeak)
peak.file <- system.file("extdata", "debchip_peaks.bed", package = "DEbPeak")
peak.df <- GetConsensusPeak(peak.file = peak.file)
peak.profile <- PeakProfile(peak.df, species = "Mouse", by = "gene", region.type = "body", nbin = 800)

#> >> preparing promoter regions...	 2023-07-02 17时21分47秒 
#> >> preparing tag matrix...		 2023-07-02 17时21分47秒 
#> >> preparing start_site regions by ... 2023-07-02 17时21分47秒
#> >> preparing tag matrix...  2023-07-02 17时21分47秒 
#> >> generating figure...		 2023-07-02 17时21分53秒 
#> >> done...			 2023-07-02 17时21分54秒 
#> >> binning method is used...2023-07-02 17时21分54秒
#> >> preparing start_site regions by gene... 2023-07-02 17时21分54秒
#> >> preparing tag matrix by binning...  2023-07-02 17时21分54秒 
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时22分02秒 
#> >> binning method is used...2023-07-02 17时22分02秒
#> >> preparing body regions by gene... 2023-07-02 17时22分02秒
#> >> preparing tag matrix by binning...  2023-07-02 17时22分02秒 
#> >> preparing matrix with extension from (TSS-20%)~(TTS+20%)... 2023-07-02 17时22分02秒
#> >> 1 peaks(0.1536098%), having lengths smaller than 800bp, are filtered... 2023-07-02 17时22分05秒
#> >> Running bootstrapping for tag matrix...		 2023-07-02 17时22分47秒