metaGeneProfile: metaGeneProfile for the GRanges objects

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

Description

An function for calculating the genomic position and generate the meta gene profile plot of the input peaks.

Usage

metaGeneProfile(
    object,
    annotation,
    include_intron = FALSE,
    title = "Meta Gene Profile",
    group = NA,
    split = FALSE,
    exlevel = NA,
    extranscript_support_level = NA,
    adjust = 1,
    nomap = FALSE
)

Arguments

object	A GRanges object which should contains all the peaks that you want to check
annotation	A path way to the annotation file. The format of the annotation file should be gff3 and downloaded from https://www.gencodegenes.org/
include_intron	A logical vector TRUE or FALSE that define whether the intronic region should be included in the position calculation or not.
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.
split	A logical vector which indicates whether the plot should show the density curve for 3'UTR, CDS 5'UTR, respectively.
exlevel	A parameter for the annotation filtering. exlevel represents the level that you would like to exclude. NA means no level filtering for the annotation file. The level from the annotations refers to how reliable this annotation is. For more information about level please check https://www.gencodegenes.org/pages/data_format.html.
extranscript_support_level	A parameter for the annotation filtering. extranscript_support_level represents the transcript_support_level that you would like to exclude (e.g. 4 and 5). NA means no transcript_support_level filtering for the annotation file. Transcripts are scored according to how well mRNA and EST alignments match over its full length. Here the number 6 means the transcript_support_level NA. For more information about level please check https://www.gencodegenes.org/pages/data_format.html.
adjust	A parameter inherit from ggplot2. A multiplicate bandwidth adjustment. This makes it possible to adjust the bandwidth while still using the a bandwidth estimator. For example, adjust = 1/2 means use half of the default bandwidth.
nomap	A logical vector. 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.

• location: Which genomic region this peak belongs to.

• Gene ID: Which gene this peak belongs to.

• Position: The relative position of each peak. This value close to 0 means this peak located close to the 5' end of the genomic feature. The position value close to one means the peak close to the 3' end of the genomic feature. Value 5 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. The position value between 0 to 1 means it located at the 5' UTR, the value close to the 1 means the position of this peak close to the 3' end of the 5' UTR. Peaks located at CDS would have a number between 1 and 2. Postion value between 2 to 3 means this peak assigned to the 3' UTR. For the peaks which can not be assignment to any annotations, they have the value 5. The list 2 includes the plot of meta gene profile.

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")

output <- metaGeneProfile(
    object = test, annotation = test_gff3,
    include_intron = FALSE
)

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