windowProfile: windowProfile for the GRanges objects

In Codezy99/cliProfiler: A package for the CLIP data visualization

Description

An function to check the position of peaks within the given GRanges windows.

Usage

windowProfile(
    object,
    annotation,
    title = "Window Profile",
    group = NA,
    nomap = FALSE
)

Arguments

object	A GRanges object which contains all the peaks that you want to check
annotation	A GRanges object that includes the customised genomic region.
title	The main title for the output meta gene profile plot.
group	The column name which contains the information of grouping for making the comparison plot. NA means all the peaks belongs to the same catagory.
nomap	A logical vector (TRUE or FALSE). It indicates whether you would like to exclude peaks that cannot assign to annotations in the plot.

Details

Here is an explanation of output meta data in the list 1:

• center: The center position of each peaks. This center position is used for calculating the position of peaks within the genomic regions.

• window_S and window_E: The boundary of the annotation that peaks are assigned.

• window_length: The length of the annotation feature that peak assigned.

• window_map: The relative position of each peak. This value close to 0 means this peak located close to the 5' end of the annotation. The position value close to one means the peak close to the 3' end. Value 3 means this peaks can not map to any annotation.

Value

A list object, the list 1 contains the information of the assignment of the peaks and their position value within the given region. The value close to 1 means the peak close to the end of region in 3' end direction. The list 2 includes the ggplot of windowProfile.

Author(s)

You Zhou, Kathi Zarnack

Examples

## Load the test data and get the path to the test gff3 file
testpath <- system.file("extdata", package = "cliProfiler")
test <- readRDS(file.path(testpath, "test.rds"))
test_gff3 <- file.path(testpath, "annotation_test.gff3")
test_gff3 <- rtracklayer::import.gff3(test_gff3)

output <- windowProfile(test, test_gff3)

Codezy99/cliProfiler documentation built on Dec. 17, 2021, 2:59 p.m.