qProject-class: qProject objects
In QuasR: Quantify and Annotate Short Reads in R

Description Details Accessors Subsetting Author(s) See Also Examples

The qProject class is a container for the meta-data (e.g. sample names, paths and names of sequence and alignment files) associated with a high-throughput sequencing experiment analyzed with QuasR.

The qProject class is returned by qAlign and stores all information on a high-throughput sequencing experiment analyzed with QuasR. qProject objects can be conveniently passed to ‘q’-functions (function name starting with the letter ‘q’). The information is stored in the following slots:

reads: a 'data.frame' with sequence read files.
reads_md5subsum: a 'data.frame' with fingerprints for sequence read files.
alignments: a 'data.frame' with alignment files.
samplesFormat: a 'character(1)' specifying the format of input files.
genome: a 'character(1)' specifying the reference genome.
genomeFormat: a 'character(1)' specifying the format of the reference genome.
aux: a 'data.frame' with auxiliary reference sequence files.
auxAlignments: a 'data.frame' with alignment files for auxiliary reference sequence files.
aligner: a 'character(1)' specifying the aligner.
maxHits: a 'numeric(1)' specifying the maximum number of alignments per sequence.
paired: a 'character(1)' specifying the paired-type; one of "no", "fr", "rf", "ff".
splicedAlignment: a 'logical(1)'; TRUE when performing spliced-alignments.
snpFile: a 'character(1)' with a file name containing SNP information.
bisulfite: a 'character(1)' defining the bisulfite type; one of "no", "dir", "undir".
alignmentParameter: a 'character(1)' with aligner command line parameters.
projectName: a 'character(1)' with the project name.
alignmentsDir: a 'character(1)' with the directory to be used to store alignment files.
lib.loc: a 'character(1)' with the library directory to use for installing of alignment index packages.
cacheDir: a 'character(1)' with a directory to use for temporary files.
alnModeID: a 'character(1)' used internally to indicate the alignment mode.

In the following code snippets, x is a qProject object.

: length(x): Gets the number of input files.

: genome(x): Gets the reference genome as a 'character(1)'. The type of genome is stored as an attribute in attr(genome(x),"genomeFormat"): "BSgenome" indicates that genome(x) refers to the name of a BSgenome package, "file" indicates that it contains the path and filename of a genome in FASTA format.
: auxiliaries(x): Gets a data.frame with auxiliary target sequences, with one row per auxiliary target, and columns "FileName" and "AuxName".
: alignments(x): Gets a list with two elements "genome" and "aux". alignments(x)$genome contains a data.frame with length(x) rows and the columns "FileName" (containing the path to bam files with genomic alignments) and "SampleName". alignments(x)$aux contains a data.frame with one row per auxiliary target sequence (with auxiliary names as row names), and length(x) columns.

In the following code snippets, x is a qProject object.

: x[i]: Get qProject object instance with i input files, where i can be an NA-free logical, numeric, or character vector.

Anita Lerch, Dimos Gaidatzis and Michael Stadler

qAlign

# copy example data to current working directory
file.copy(system.file(package="QuasR", "extdata"), ".", recursive=TRUE)

# create alignments
sampleFile <- "extdata/samples_chip_single.txt"
genomeFile <- "extdata/hg19sub.fa"
auxFile <- "extdata/auxiliaries.txt"

proj <- qAlign(sampleFile, genomeFile, auxiliaryFile=auxFile)
proj

# alignment statistics using a qProject
alignmentStats(proj)

# alignment statistics using bam files
alignmentStats(alignments(proj)$genome$FileName)
alignmentStats(unlist(alignments(proj)$aux))