write2FASTA {ChIPpeakAnno} | R Documentation

## Write sequences to a file in fasta format

### Description

Write the sequences obtained from getAllPeakSequence to a file in fasta format leveraging writeFASTA in Biostrings package. FASTA is a simple file format for biological sequence data. A FASTA format file contains one or more sequences and there is a header line which begins with a > proceeding each sequence.

### Usage

    write2FASTA(mySeq, file="", width=80)

### Arguments

`mySeq` | GRanges with varibles name and sequence ,e.g., results obtained from getAllPeakSequence
`file` | Either a character string naming a file or a connection open for reading or writing. If "" (the default for write2FASTA), then the function writes to the standard output connection (the console) unless redirected by sink
`width` | The maximum number of letters per line of sequence

### Value

Output as FASTA file format to the naming file or the console.

### Author(s)

Lihua Julie Zhu

### Examples

    peaksWithSequences = GRanges(seqnames=c("1", "2"),
    IRanges(start=c(1000, 2000),
    end=c(1010, 2010),
    names=c("id1", "id2")),
    sequence= c("CCCCCCCCGGGGG", "TTTTTTTAAAAAA"))

    write2FASTA(peaksWithSequences, file="testseq.fasta", width=50)

[Package ChIPpeakAnno version 3.14.2 Index]