R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
All

Data Type

Packages
Functions
Images
Data set

Classification

Results 1 - 10 of 10 found.
[1] < 1 > [1] Sort:

SeqCNAInfo-class (Package: seqCNA) : Class code{"SeqCNAInfo"

A structure that contains information on depth of coverage (DOC), genome build, and summarization window size and position. If applicable, it also contains paired normal DOC. If paired-end mapping (PEM) was used in the alignment, DOCs are broken down by read type. Further processing with seqCNA functions of these objects, attach filtering information, and normalized, segmented and called profiles.

● Data Source: BioConductor
● Keywords: classes
● Alias: SeqCNAInfo-class, summary,SeqCNAInfo-method
● 0 images

applyFilters (Package: seqCNA) :

The available filters are: PEM-based (only for paired-end data), trimming of extreme values, mappability-based and common CNVs.

● Data Source: BioConductor
● Keywords: Filtering
● Alias: applyFilters
● 0 images

applyThresholds (Package: seqCNA) :

Given a set of thresholds and the copy number of the lower resulting range, copy numbers are called.

● Data Source: BioConductor
● Keywords: Calling
● Alias: applyThresholds
● 0 images

plotCNProfile (Package: seqCNA) :

The plotted elements depend on the processing applied on the SeqCNAInfo-class object.

● Data Source: BioConductor
● Keywords: Output
● Alias: plotCNProfile
● 1 images

readSeqsumm (Package: seqCNA) :

The function reads the seqsumm_out.txt file(s) from the indicated directories and builds a SeqCNAInfo-class object, with read count (RC) and genomic information.

● Data Source: BioConductor
● Keywords: Summarization
● Alias: readSeqsumm
● 0 images

runGLAD (Package: seqCNA) :

The function calls the corresponding function in the GLAD library with appropriate parameters.

● Data Source: BioConductor
● Keywords: Segmentation
● Alias: runGLAD
● 0 images

runSeqnorm (Package: seqCNA) :

The seqnorm method performs several regressions on homogeneous regions of the tumoural genomic profile.

● Data Source: BioConductor
● Keywords: Normalization
● Alias: runSeqnorm
● 0 images

runSeqsumm (Package: seqCNA) :

The function calls the seqsumm program to summarize aligned reads into genomic windows. The results are output to a file called seqsumm_out.txt.

● Data Source: BioConductor
● Keywords: Summarization
● Alias: runSeqsumm
● 0 images

seqCNA-package (Package: seqCNA) :

Fast summarization, extensive filtering and improved normalization

● Data Source: BioConductor
● Keywords:
● Alias: seqCNA, seqCNA-package
● 0 images

writeCNProfile (Package: seqCNA) :

The output columns depend on the processing applied on the SeqCNAInfo-class object.

● Data Source: BioConductor
● Keywords: Output
● Alias: writeCNProfile
● 0 images