extract_3ss_motif: Extract the acceptor splice site motif for MaxEntScan web...

In monahton/GencoDymo: Data Extraction and Manipulation from the GENCODE Database

Description

This function takes a data frame of intron coordinates and the full genome sequence of a particular species and return a "bed-file" structured data frame containing the motif coordinates, their corresponding transcripts id and intron number and the motif sequence which are also saved as a fasta file in the working directory. The fasta file can be uploaded to MaxEntScan::3ss web tool for the retrieval of the scores of acceptor splice sites.

Usage

extract_3ss_motif(input,genome)

Arguments

input	The name of the data frame containing intron coordinates
genome	The full genome sequence of a particular species. The default value is the human genome sequence of the hg38 assembly

Value

A data frame with motif coordinates and their sequences

See Also

extract_5ss_motif

Examples

extract_3ss_motif(introns_df, genome=BSgenome.Hsapiens.UCSC.hg38)

monahton/GencoDymo documentation built on Nov. 29, 2021, 9:16 a.m.