QuasR (version 1.12.0)

qProject-class: qProject objects

Description

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.

Details

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: [object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object]

See Also

qAlign

Examples

# 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))