spliceSiteProfile: spliceSiteProfile for the GRanges objects

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

Description

An function to check the enrichment of peaks around the splice sites in a absolute distance.

Usage

spliceSiteProfile(
    object,
    annotation,
    title = "Splice Site Profile",
    exlevel = NA,
    extranscript_support_level = NA,
    exon_length_filtering = TRUE,
    intron_length_filtering = TRUE,
    flanking = 150,
    bin = 30
)

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.
exon_length_filtering	The exon_length_filtering should be a logical value which indicated whether user would like to exclude the exons that have a length less than flanking value. Set this parameter to TRUE to turn on this filtering step.
intron_length_filtering	The intron_length_filtering should be a logical value which indicated whether user would like to exclude the introns that have a length less than flanking value. Set this parameter to TRUE to turn on this filtering step.
flanking	The size of the flanking windows that you would like to check. Flanking=5 will give you the result of the 10+1nt windows around the center of peaks.
bin	A number that indicates how many bins would you like to use in the histogram.

Value

A list object, the list 1 contains the information of the position of peaks around 5' or 3' splice sites. The list 2 includes the plot of spliceSiteProfile

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 <- spliceSiteProfile(test, test_gff3,
    flanking = 200, bin = 40
)

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