mixed_circ_tss_calculation: Function for reading exon intron and promoter structure from...

In PayamEmami/mixedcirc: Circadian rhythm analysis using mixed models

Function for reading exon intron and promoter structure from a given bed or GFF file

Description

Function for reading exon intron and promoter structure from a given bed or GFF file

Usage

readTranscriptFeatures(location,remove.unusual=TRUE,
                              up.flank=1000,down.flank=1000,unique.prom=TRUE)

Arguments

location	location of the bed file with 12 or more columns. The file can end in .gz, .bz2, .xz, or .zip and/or start with http:// or ftp://. If the file is not compressed it can also start with https:// or ftps://. or location of GFF file
gff	If TRUE, location is assumed to be GFF file
id	This is supposed to be a column of GFF file showing the symbol or id of each genes
remove.unusual	remove the chromomesomes with unsual names, mainly random chromsomes etc (only in bed file)
up.flank	up-stream from TSS to detect promoter boundaries
down.flank	down-stream from TSS to detect promoter boundaries
unique.prom	get only the unique promoters, promoter boundaries will not have a gene name if you set this option to be TRUE

Details

This function is an extension of readTranscriptFeatures function from genomation package that now supports GFF file. The idea behind GFF features is that they are calculated on gene levels in contrast to transcript levels. Therefore the parameter id must be supplied together with GFF file so that the function knows what genes to use. For each unique genes, the function collapse the coordinate to contain all the genomics features. These new coordinates are used to calculate TSS and promoter regions.

Value

a GRangesList containing locations of exon/intron/promoter/TSS

Note

one bed track per file is only accepted, the bed files with multiple tracks will cause en error.

Examples

my.bed12.file = system.file("extdata/chr21.refseq.hg19.bed", package = "genomation")
my.bed12.file
feats = mixed_circ_tss_calculation(my.bed12.file)
names(feats)
sapply(feats, head)

gff.file = system.file('extdata/chr21.refseq.hg19.gtf', package='genomation')
feats = mixed_circ_tss_calculation(gff.file,gff=TRUE)
names(feats)

PayamEmami/mixedcirc documentation built on Jan. 15, 2025, 5:36 p.m.