geneTypeProfile: geneTypeProfile for the GRanges objects

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

Description

An function to check the gene type belonging for the peaks.

Usage

geneTypeProfile(
    object,
    annotation,
    title = "Gene Type Profile",
    exlevel = NA,
    extranscript_support_level = NA
)

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/
title	The main title for the output meta gene profile plot.
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.

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.

• geneType: The gene type of the gene that input peak belongs to.

• Gene_ID: The gene ID of the gene that input peak belongs to.

Value

A list object, the list 1 contains the information of the assignment of the peaks and the gene type of their located genes. The list 2 includes the plot of geneTypeProfile

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 <- geneTypeProfile(test, test_gff3)

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