checkBedFasta: Function to control Bed and FASTA files compatibility.

In 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)

Example output

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit

Loading required package: ggplot2
Loading required package: plyr

Attaching package: 'plyr'

The following object is masked from 'package:XVector':

    compact

The following object is masked from 'package:IRanges':

    desc

The following object is masked from 'package:S4Vectors':

    rename

Loading required package: openxlsx
- Checking bed file, mandatory columns:
 OK
- Checking bed file, duplicated feature IDs:
 OK
- Checking bed file, duplicated feature locations:
 OK
- Checking bed file, start and end values:
 OK
- Checking bed-fasta chromosome consistency:
 OK
- Checking bed-fasta genomic coordinates consistency:
 OK
Warning message:
system call failed: Cannot allocate memory 

TarSeqQC documentation built on Nov. 8, 2020, 6:03 p.m.