R Package To Handle Files From Genomic Data GenomicTools.fileHandler is a loose collection of I/O Functions Needed in Genomic Data Analysis

Description

Author(s)

Daniel Fischer

Maintainer: Daniel Fischer <daniel.fischer@luke.fi>

Example Gene Annotation in Bed-Format

Description

This file contains some example lines to represent a typical bed file that can be used to try the corresponding functions.

Format

A file with three column Chr, Start and End.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.bed", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Sequencing Reads in fasta-Format

Description

This file contains some example reads to represent a typical fasta file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.fasta", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Sequencing Reads in fastq-Format

Description

This file contains some example reads to represent a typical fastq file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.fastq", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Gene Annotation in gff-Format

Description

This file contains some example gene annotations to represent a typical gff file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.gff", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Gene Annotation in gtf-Format

Description

This file contains some example gene annotations to represent a typical gtf file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.gtf", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Variant data in ped/map-Format

Description

This file contains some example variants to represent a typical ped/map file pair that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.ped", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Variant data in vcf-Format

Description

This file contains some example variants to represent a typical vcf file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example.vcf", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Example Gene Annotation in zipped gtf-Format

Description

This file contains some example gene annotations to represent a typical zipped gtf file that can be used to try the corresponding functions.

Details

The file is locate din the /extdata folder of the package and is accessible after installation via system.file("extdata","example2.gtf.gz", package="GenomicTools.fileHandler")

Author(s)

Daniel Fischer

Exporting a Bed File.

Description

This function exports a standard bed file.

Usage

exportBed(x, file = NULL, header = FALSE)

Arguments

Details

This function exports a data.frame to a standard bed file. If no file name is given, the variable name will be used instead.

Value

A bed file

Author(s)

Daniel Fischer

Examples

novelBed <- data.frame(Chr=c(11,18,3),
                      Start=c(72554673, 62550696, 18148822),
                      End=c(72555273, 62551296, 18149422),
                      Gene=c("LOC1", "LOC2", "LOC3"))

# Create a temporary file to where the output of the function is stored
myfile <- file.path(tempdir(), "myLocs.bed")

exportBed(novelBed, file=myfile)
exportBed(novelBed, file=myfile, header=TRUE)

Exporting a Fasta File.

Description

This function exports a standard fasta file.

Usage

exportFA(fa, file = NULL)

Arguments

Details

This function exports a fasta object to a standard fasta file. If no file name is given, the variable name will be used instead.

Value

A fasta file

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.fasta", package="GenomicTools.fileHandler")
 # Import the example fasta file  
   fastaFile <- importFA(file=fpath)
   newFasta <- fastaFile[1:5]
   
myfile <- file.path(tempdir(), "myLocs.fa")
   
  exportFA(newFasta, file=myfile)

Importing a Bed File.

Description

This function imports a standard bed file

Usage

importBed(file, header = FALSE, sep = "\t")

Arguments

Details

This function imports a standard bed-file into a data.frame. It is basically a convenience wrapper around read.table. However, if no header lines is given, this function automatically assigns the column names, as they are given in the bed-specification on the Ensembl page here: https://www.ensembl.org/info/website/upload/bed.html

Value

A data.frame

Author(s)

Daniel Fischer

See Also

[exportBed], [read.table]

Examples

   
 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.bed", package="GenomicTools.fileHandler")
 # Import the example bed file  
   bedFile <- importBed(file=fpath)
 

Import a Tab Delimited Blast Output File

Description

This function imports a tab delimited blast output.

Usage

importBlastTab(file)

Arguments

Details

This function imports a tab delimited blast output file, currently the same as read.table

Value

A data.frame

Author(s)

Daniel Fischer

Importing a Fasta File.

Description

This function imports a standard fasta file

Usage

importFA(file)

Arguments

Details

This function imports a standard fasta file. Hereby, it does not matter if the identifier and sequence are alternating or not, as the rows starting with '>' are used as identifer.

The example file was downloaded from here and was then further truncated respective transformed to fasta format:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase3/data/HG00096/sequence_read/

Value

An object of class fa containing the sequences. The names correspond to the sequence names given in the fasta file.

Author(s)

Daniel Fischer

See Also

print.fa, summary.fa

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.fasta", package="GenomicTools.fileHandler")
 # Import the example fasta file  
   fastaFile <- importFA(file=fpath)
 

Importing a Fastq File.

Description

This function imports a standard fastq file

Usage

importFQ(file)

Arguments

Details

This function imports a standard fastq file that consists out of blocks of four lines per entry

Value

An object of class fq containing the sequences and the quality meausure. The names correspond to the sequence names given in the fasta file.

Author(s)

Daniel Fischer

See Also

print.fq, summary.fq

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.fastq", package="GenomicTools.fileHandler")
 # Import the example fastq file  
   fastqFile <- importFQ(file=fpath)
 

Import from FeatureCounts

Description

This functions imports the output from FeatureCounts

Usage

importFeatureCounts(file, skip = 0, headerLine = 2)

Arguments

Details

FeatureCounts produces two files, the txt that contain the expression values and then the summary that containts all the information about the mapping statistics. This function imports both and stores them in a corresponding list.

Value

A list with expValues, geneInfo and summary

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","featureCountsExample.txt", package="GenomicTools.fileHandler")
 # Import the example featureCounts file  
   fcFile <- importFeatureCounts(file=fpath)
 

importGFF

Description

Import a GFF file

Usage

importGFF(file, skip = "auto", nrow = -1, use.data.table = TRUE,
  level = "gene", features = NULL, num.features = c("FPKM", "TPM"),
  print.features = FALSE, merge.feature = NULL, merge.all = TRUE,
  class.names = NULL, verbose = TRUE)

Arguments

Details

This function imports a standard gff file.

Value

A gff object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.gff", package="GenomicTools.fileHandler")
 # Import the example gff file  
   importGFF(fpath)
   

importGFF3

Description

Import a GFF3 file

Usage

importGFF3(gff, chromosomes)

Arguments

Details

This function imports a standard gff3 file.

Value

A gff object

Author(s)

Daniel Fischer

Import a GTF File

Description

This function imports a gtf file.

Usage

importGTF(file, skip = "auto", nrow = -1, use.data.table = TRUE,
  level = "gene", features = NULL, num.features = c("FPKM", "TPM"),
  print.features = FALSE, merge.feature = NULL, merge.all = TRUE,
  class.names = NULL, verbose = TRUE)

Arguments

Details

This function imports a gtf file. The features names to be imported are defined in features, several features are then provided as vector. A list of available feature can beprinted, by setting print.features=TRUE.

The skip option allows to skip a given number of rows, the default is, however, auto. In that case, all rows that start with the # symbol are skipped.

In case a set of expression values given in gtf format should be imported and to be merged into a single data table, the feature that should be used for merging can be provided to the merge.feature option. In that case the function expects a folder in file and it will import all gtfs located in that folder and merges them according to the merge.feature option. With the option class.names a vector of prefixes for the merged features can be provided. If this is kept empty, then the filenames of the gtf will be used instead (without gtf extension).

By default the function imprts all features in column 9 as string character. However, for common labels (FPKM and TPM) the class type is set automatically to numeric. Additional numerical feature names can be defined with the num.feature option.

Value

A gtf object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.gtf", package="GenomicTools.fileHandler")
 # Same file, but this time as gzipped version
   fpath.gz <- system.file("extdata","example2.gtf.gz", package="GenomicTools.fileHandler")
   
 # Import the example gtf file  
   importGTF(fpath, level="transcript", features=c("gene_id","FPKM"))
   
 ## Not run: 
 # For the current you need to have zcat installed (should be standard on a Linux system)
   importGTF(fpath.gz, level="transcript", features=c("gene_id","FPKM"))
   
## End(Not run)
 

importPED

Description

Import a PED/MAP file pair

Usage

importPED(file, n, snps = NULL, which, split = "\t| +", sep = ".",
  na.strings = "0", lex.order = FALSE, verbose = TRUE)

Arguments

Details

This function is to a large extend taken from snpStat::read.pedmap, but here is internally the data.table::fread function used that resulted in much faster file processing.

To import the data, the ped file can be provided to the file option and the map file to the snps option. If no option is given to snps and the file option is provided without any file extension, then the ped/map extension are automaticall added

Value

a pedmap object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   pedPath <- system.file("extdata","example.ped", package="GenomicTools.fileHandler")
   mapPath <- system.file("extdata","example.map", package="GenomicTools.fileHandler")
 # Import the example ped/map files  
   importPED(file=pedPath, snps=mapPath)

importSTARLog

Description

Import the Log-File from STAR

Usage

importSTARLog(dir, recursive = TRUE, log = FALSE, finalLog = TRUE,
  verbose = TRUE)

Arguments

Details

This function imports the Log file from STAR

Value

a data frame

Author(s)

Daniel Fischer

importVCF

Description

Import a VCF function

Usage

importVCF(file, na.seq = "./.")

Arguments

Details

This function imports a VCF file.

In case the logicl flag 'phased' is set to TRUE then the genotypes are expected to be in the format 0|0, otherwise they are expected to be like 0/1 .

The example file was downloaded from here:

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/pilot_data/release/2010_07/exon/snps/

Value

A vcf object

Author(s)

Daniel Fischer

Examples

 # Define here the location on HDD for the example file
   fpath <- system.file("extdata","example.vcf", package="GenomicTools.fileHandler")
 # Import the example vcf file  
   importVCF(fpath)

importXML

Description

Import an Blast XML file

Usage

importXML(folder, seqNames = NULL, which = NULL, idTH = 0.8,
  verbose = TRUE)

Arguments

Details

This function imports XML files as provided as Blast output, it is mainly aimied to import the output of the hoardeR package

Value

An XML object

Author(s)

Daniel Fischer

plotTotalReads

Description

Plot the total reads

Usage

plotTotalReads(STARLog)

Arguments

Details

This function plots the total reads from a STARlog object

Part of the diagnostic plot series for of the STARLog. The function accepts also a list of STARLogs and creates then comparative boxplots

Value

A plot

Author(s)

Daniel Fischer

plotUniquelyMappedReads

Description

Plot the uniquely mapped reads

Usage

plotUniquelyMappedReads(STARLog)

Arguments

Details

This function plots the percenage of uniquely reads from a STARlog object

Part of the diagnostic plot series for of the STARLog. The function accepts also a list of STARLogs and creates then comparative boxplots

Value

A plot

Author(s)

Daniel Fischer

prereadGTF

Description

Preread a gtf file and prints features of it for importing it.

Usage

prereadGTF(file, nrow = 1000, skip = "auto")

Arguments

Details

This function reads in a gtf file and prints its features for the import step.

By default this function only imports the first 1000 rows, in case all rows should be imported set nrow=-1.

The number to skip in the beginning can be adjusted by the skip option. The default is here auto so that the function can identify the correct amount of header rows. Hence, this option should be changed only, if there is a good reason.

Value

A list of available features

Author(s)

Daniel Fischer

Print a bed Object

Description

Prints a bed object.

Usage

## S3 method for class 'bed'
print(x, n = 6, ...)

Arguments

Details

The print function displays a bed object

Author(s)

Daniel Fischer

Print a fa Object

Description

Prints a fa object.

Usage

## S3 method for class 'fa'
print(x, n = 2, seq.out = 50, ...)

Arguments

Details

The print function displays a fa object

Author(s)

Daniel Fischer

Print a featureCounts Object

Description

Prints an featureCounts object.

Usage

## S3 method for class 'featureCounts'
print(x, ...)

Arguments

Details

The print function displays a featureCounts object

Author(s)

Daniel Fischer

Print a fq Object

Description

Prints a fq object.

Usage

## S3 method for class 'fq'
print(x, n = 2, seq.out = 50, print.qual = TRUE, ...)

Arguments

Details

The print function displays a fa object

Author(s)

Daniel Fischer

Print a gtf Object

Description

Prints a gtf object.

Usage

## S3 method for class 'gtf'
print(x, n = 6, ...)

Arguments

Details

The print function displays a bed object

Author(s)

Daniel Fischer

Print a pedMap Object

Description

Prints an pedMap object.

Usage

## S3 method for class 'pedMap'
print(x, n = 6, m = 6, ...)

Arguments

Details

The print function displays a pedMap object

Author(s)

Daniel Fischer

Print a vcf Object

Description

Prints an vcf object.

Usage

## S3 method for class 'vcf'
print(x, n = 6, m = 6, fullHeader = FALSE, ...)

Arguments

Details

The print function displays a vcf object

Author(s)

Daniel Fischer

Summary of a STARLog Object

Description

Summarizes a STARLog object.

Usage

## S3 method for class 'STARLog'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a STARLog object

Author(s)

Daniel Fischer

Summary of a bed Object

Description

Summarizes a bed object.

Usage

## S3 method for class 'bed'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a bed object

Author(s)

Daniel Fischer

Summary of a fa Object

Description

Summarizes a fa object.

Usage

## S3 method for class 'fa'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a fa object

Author(s)

Daniel Fischer

Summary of a featureCounts Object

Description

Summarizes a featureCounts object.

Usage

## S3 method for class 'featureCounts'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a featureCounts object

Author(s)

Daniel Fischer

Summary of a fq Object

Description

Summarizes a fq object.

Usage

## S3 method for class 'fq'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a fq object

Author(s)

Daniel Fischer

Summary of a gtf Object

Description

Summarizes a gtf object.

Usage

## S3 method for class 'gtf'
summary(object, ...)

Arguments

Details

The summary function displays an informative summary of a gtf object

Author(s)

Daniel Fischer