extendTSSFromDataFrame: Extend TSS

In jokergoo/rGREAT: GREAT Analysis - Functional Enrichment on Genomic Regions

Extend TSS

Description

Extend TSS

Usage

extendTSSFromDataFrame(df, seqlengths, genome = NULL,
    strand = NULL, gene_id = NULL,
    gene_id_type = NULL, verbose = great_opt$verbose, ...)

Arguments

df	A bed-like data frame where the first three columns should be chromosomes, start positions, end positions. It does not matter whether regions correspond to genes or TSS.
seqlengths	A named vector of chromosome lengths.
genome	UCSC genome can be set here, then seqlengths will be automatically retrieved from UCSC server.
strand	The strand information can be provided in df as a column named "strand" or as a column with "+"/"-"/"*", or the strand information can be provided as a vector and be assigined to this argument.
gene_id	The gene ID information can be provided in df as a column named "gene_id", or it can be provided as a vector and be assigned to this argument.
gene_id_type	Gene ID types in df. You need to set this argument if you use built-in gene sets in great so that genes can be correctly mapped. The value can only be one of "SYMBOL", "ENTREZ", "ENSEMBL" and "REFSEQ".
verbose	Whether to print messages.
...	All pass to extendTSS.

Value

A GRanges object with one meta column 'gene_id'.

Examples

# There is no example
NULL

jokergoo/rGREAT documentation built on March 28, 2024, 5:31 a.m.