Extend TSS — extendTSSFromDataFrame • rGREAT

Extend TSS

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.

A GRanges object with one meta column 'gene_id'.

# There is no example
NULL
#> NULL