QDNAseq-defunct
(Package: QDNAseq) :
Defunct functions in package sQuote{QDNAseq
These functions are defunct and no longer available.
● Data Source:
BioConductor
● Keywords:
● Alias: downloadBinAnnotations
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Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
● Data Source:
BioConductor
● Keywords: package
● Alias: QDNAseq, QDNAseq-package
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QDNAseqCopyNumbers
(Package: QDNAseq) :
Container for QDNAseq read count data
Container for QDNAseq read count data
● Data Source:
BioConductor
● Keywords: classes
● Alias: QDNAseqCopyNumbers, QDNAseqCopyNumbers-class
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QDNAseqReadCounts
(Package: QDNAseq) :
Container for QDNAseq read count data
Container for QDNAseq read count data
● Data Source:
BioConductor
● Keywords: classes
● Alias: QDNAseqReadCounts, QDNAseqReadCounts-class
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QDNAseqSignals
(Package: QDNAseq) :
A parent class for containers of QDNAseq data
A parent class for containers of QDNAseq data
● Data Source:
BioConductor
● Keywords: classes
● Alias: QDNAseqSignals, QDNAseqSignals-class
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addPhenodata
(Package: QDNAseq) :
Adds phenotype data from a file to a QDNAseqReadCounts or a
Adds phenotype data from a file to a QDNAseqReadCounts or a QDNAseqCopyNumbers object.
● Data Source:
BioConductor
● Keywords: IO, file
● Alias: addPhenodata
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applyFilters
(Package: QDNAseq) :
Adjusts the filtering on which bins are used
Adjusts the filtering on which bins are used.
● Data Source:
BioConductor
● Keywords: manip
● Alias: applyFilters
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binReadCounts
(Package: QDNAseq) :
Calculate binned read counts from a set of BAM files
Calculate binned read counts from a set of BAM files.
● Data Source:
BioConductor
● Keywords: IO, file
● Alias: binReadCounts
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callBins
(Package: QDNAseq) :
Call aberrations from segmented copy number data
Call aberrations from segmented copy number data.
● Data Source:
BioConductor
● Keywords: manip
● Alias: callBins
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compareToReference
(Package: QDNAseq) :
Divide binned read counts with those of reference samples
Divide binned read counts with those of reference samples.
● Data Source:
BioConductor
● Keywords: manip
● Alias: compareToReference
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