extract_3ss_motif: Extract the acceptor splice site motif for MaxEntScan web...
In monahton/GencoDymo: Data Extraction and Manipulation from the GENCODE Database
View source: R/extract_maxentscan_motifs.R
extract_3ss_motif R Documentation
Extract the acceptor splice site motif for MaxEntScan web tool
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 Dec. 13, 2024, 1:23 a.m.
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View source: R/extract_maxentscan_motifs.R
| extract_3ss_motif | R Documentation |
Extract the acceptor splice site motif for MaxEntScan web tool
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)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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