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

Description Usage Arguments Details Value Author(s) Examples

An function to check the position of peaks in the intronic region.

intronProfile(
    object,
    annotation,
    title = "Intron Profile",
    group = NA,
    exlevel = NA,
    extranscript_support_level = NA,
    maxLength = NA,
    minLength = NA,
    nomap = FALSE
)

`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.
`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.
`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.
`maxLength`	A numeric value which indicate the maximum value of exon length for the annotation filtering. Or a NA which will turn off the max length annotation filtering.
`minLength`	A numeric value which indicate the minimum value of exon length for the annotation filtering. Or a NA which will turn off the min length annotation filtering.
`nomap`	A logical vector (TRUE or FALSE). It indicates whether you would like to exclude peaks that cannot assign to annotations in the plot.

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.
Intron_S and Intron_E: The location of 5' and 3' splice sites (SS) of the intron.
Intron_length: The length of the intron that peak assigned.
Intron_transcript_id: The transcript ID for the intron.
Intron_map: The relative position of each peak. This value close to 0 means this peak located close to the 5' SS. The position value close to one means the peak close to the 3' SS. Value 3 means this peaks can not map to any annotation.

A list object, the list 1 contains the information of the assignment of the peaks and their position value within the intron. The value close to 1 means the peak close to the 3' splice site. The list 2 includes the plot of intronProfile.

You Zhou, Kathi Zarnack

## 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 <- intronProfile(test, test_gff3)