R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Data Type

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Functions
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Classification

Results 1 - 10 of 16 found.
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NGS.CNV (Package: saasCNV) :

All analysis steps are integrate into a pipeline. The results, including visualization plots are placed in a directory as specified by user.

● Data Source: CranContrib
● Keywords: CNV, NGS, pipeline
● Alias: NGS.CNV
● 0 images

GC.adjust (Package: saasCNV) :

This function adjusts log2ratio by GC content using LOESS.

● Data Source: CranContrib
● Keywords: CNV, GC content
● Alias: GC.adjust
● 0 images

merging.segments (Package: saasCNV) :

It is an option to merge adjacent segments, for which the median values in either or both log2ratio and log2mBAF dimensions are not substantially different. For WGS and SNP array, it is recommended to do so.

● Data Source: CranContrib
● Keywords: merge, segmentation
● Alias: merging.segments
● 0 images

joint.segmentation (Package: saasCNV) :

We employ the algorithm developed by (Zhang et al., 2010) to perform joint segmentation on log2ratio and log2mBAF dimensions. The function outputs the starting and ending points of each CNV segment as well as some summary statistics.

● Data Source: CranContrib
● Keywords: CBS, joint segmentation, segmentation
● Alias: joint.segmentation
● 0 images

snp.refine.boundary (Package: saasCNV) :

Refine the segment boundaries based on the grid of heterozygous probes by all probes with LRR data. We do not recommend to perform this step except in the case that the segment boundaries need to be aligned well on the same grid of probes for downstream analysis.

● Data Source: CranContrib
● Keywords: CNV, SNP array
● Alias: snp.refine.boundary
● 0 images

cnv.data (Package: saasCNV) :

Transform read depth information into log2ratio and log2mBAF that we use for joint segmentation and CNV calling.

● Data Source: CranContrib
● Keywords: CNV
● Alias: cnv.data
● 0 images

vcf2txt (Package: saasCNV) :

It parses a VCF file and extract necessary information for CNV analysis.

● Data Source: CranContrib
● Keywords: vcf
● Alias: vcf2txt
● 0 images

cnv.call (Package: saasCNV) :

Assign SCNA state to each segment directly from joint segmentation or from the results after segments merging step.

● Data Source: CranContrib
● Keywords: CNV, CNV call
● Alias: cnv.call
● 0 images

SNP.CNV (Package: saasCNV) :

All analysis steps are integrate into a pipeline. The results, including visualization plots are placed in a directory as specified by user.

● Data Source: CranContrib
● Keywords: CNV, SNP array, pipeline
● Alias: SNP.CNV
● 0 images

saasCNV-package (Package: saasCNV) :

Perform joint segmentation on two signal dimensions derived from total read depth (intensity) and allele specific read depth (intensity) for whole genome sequencing (WGS), whole exome sequencing (WES) and SNP array data.

● Data Source: CranContrib
● Keywords:
● Alias: saasCNV, saasCNV-package
● 0 images