readGeneInput {GeneRegionScan} | R Documentation

## Standardize reading of gene inputs

### Description

Internal function that will standardise the input of the many different form of sequences that can be used in Bioconductor.

### Usage

    readGeneInput(gene, genename=NULL, verbose=TRUE)

### Arguments

`gene` | A number of gene sequences as DNAString, DNAStringSets or, character-vectors with sequence.
`genename` | Optional character string specifying a gene name to include in the plot. If not included and a FASTA sequence is given, it will default to the name in the FASTA sequence. Otherwise it will default to 'Unknown genename'.
`verbose` | TRUE or FALSE.

### Details

This function is not meant to be run directly by the user. It will take a number of genes either as a vector of characters, a path to a FASTA format file, as a DNAstrings or DNAStringSet. It will then output them in FASTA format for use with other functions. Optional variable genename forces a new name.

The primary objective of this function is to make the sequence input simpler for other functions.

### Value

A list of all sequences and their names, in exactly the same format as obtained with the deprecated function readFASTA.

### Author(s)

Lasse Folkersen

### See Also

`geneRegionScan`, `plotOnGene`

### Examples

    	somegene<-"ATACCTTGTAGGACCTGATGATAGATGCATAGTAATATCGTA"
    	genename<-"My favourite gene"
    	GeneRegionScan:::readGeneInput(somegene,genename=genename)

[Package GeneRegionScan version 1.40.0 Index]