checkBedFasta: Function to control Bed and FASTA files compatibility.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

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)

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.