readGeneInput {GeneRegionScan} | R Documentation |
Internal function that will standardise the input of the many different form of sequences that can be used in Bioconductor.
readGeneInput(gene, genename=NULL, verbose=TRUE)
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. |
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.
A list of all sequences and their names, in exactly the same format as obtained with the deprecated function readFASTA.
Lasse Folkersen
somegene<-"ATACCTTGTAGGACCTGATGATAGATGCATAGTAATATCGTA" genename<-"My favourite gene" GeneRegionScan:::readGeneInput(somegene,genename=genename)