checkBedFasta {TarSeqQC} | R Documentation

## Function to control Bed and FASTA files compatibility.

### Description

`checkBedFasta` checks the compatibility of a Bed file and a Fasta file. The functions first will control the consistency of the Bed file in terms of duplicated positions or feature's IDs and correct definition of start-end values. Then, the method will control the consistency between the specified features and the reference file. During its execution, several testing messages will be printed.

### Usage

    checkBedFasta(bedFile, fastaFile)

### Arguments

`bedFile` | Character indicating the bed file full path.
`fastaFile` | Character indicating the full path to the genome reference file.

### Value

NULL

### Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

### See Also

`TargetExperiment-class`

### Examples

    ##Define the bed and fasta file full paths
    bedFile<-system.file("extdata", "mybed.bed", package="TarSeqQC", mustWork=TRUE)
    fastaFile<-system.file("extdata", "myfasta.fa", package="TarSeqQC",
        mustWork=TRUE)
    ##Checking the bed-fasta consistency
    checkBedFasta(bedFile, fastaFile)

[Package TarSeqQC version 1.10.0 Index]