R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
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Classification

Results 1 - 10 of 71 found.
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ASEset-barplot (Package: AllelicImbalance) : barplot ASEset objects

Generates barplots for ASEset objects. Two levels of plotting detail are provided: a detailed barplot of read counts by allele useful for fewer samples and SNPs, and a less detailed barplot of the fraction of imbalance, useful for more samples and SNPs.

● Data Source: BioConductor
● Keywords: barplot
● Alias: ASEset-barplot, barplot, barplot,ASEset-method
● 1 images

ASEset-class (Package: AllelicImbalance) : ASEset objects

Object that holds allele counts, genomic positions and map-bias for a set of SNPs

● Data Source: BioConductor
● Keywords: ASEset, class
● Alias: ASEset, ASEset-class, alleleCounts, alleleCounts,ASEset-method, alleleCounts<-, alleleCounts<-,ASEset-method, alt, alt,ASEset-method, alt<-, alt<-,ASEset,ANY-method, altExist, altExist,ASEset-method, aquals, aquals,ASEset-method, aquals<-, aquals<-,ASEset-method, arank, arank,ASEset-method, countsPerSample, countsPerSample,ASEset-method, countsPerSnp, countsPerSnp,ASEset-method, fraction, fraction,ASEset-method, frequency, frequency,ASEset-method, genotype, genotype,ASEset-method, genotype<-, genotype<-,ASEset-method, mapBias, mapBias,ASEset-method, mapBias<-, mapBias<-,ASEset-method, maternalAllele, maternalAllele,ASEset-method, paternalAllele, paternalAllele,ASEset-method, phase, phase,ASEset-method, phase<-, phase<-,ASEset-method, ref, ref,ASEset-method, ref<-, ref<-,ASEset,ANY-method, refExist, refExist,ASEset-method
● 0 images

ASEset-filters (Package: AllelicImbalance) : genotype filter methods

useful genotype filters

● Data Source: BioConductor
● Keywords: filter
● Alias: ASEset-filters, hetFilt, hetFilt,ASEset-method
● 0 images

ASEset-gbarplot (Package: AllelicImbalance) : gbarplot ASEset objects

Generates gbarplots for ASEset objects. Two levels of plotting detail are provided: a detailed gbarplot of read counts by allele useful for fewer samples and SNPs, and a less detailed gbarplot of the fraction of imbalance, useful for more samples and SNPs.

● Data Source: BioConductor
● Keywords: gbarplot
● Alias: ASEset-gbarplot, gbarplot, gbarplot,ASEset-method
● 0 images

ASEset-glocationplot (Package: AllelicImbalance) : glocationplot ASEset objects

plotting ASE effects over a specific genomic region using Gviz functionality

● Data Source: BioConductor
● Keywords: glocationplot
● Alias: ASEset-glocationplot, glocationplot, glocationplot,ASEset-method
● 2 images

ASEset-gviztrack (Package: AllelicImbalance) : ASEset-gviztrack ASEset objects

plotting ASE effects over a specific genomic region

● Data Source: BioConductor
● Keywords: ASEDAnnotationTrack, CoverageDataTrack
● Alias: ASEDAnnotationTrack, ASEDAnnotationTrack,ASEset-method, ASEset-gviztrack, CoverageDataTrack, CoverageDataTrack,ASEset-method
● 0 images

ASEset-scanForHeterozygotes (Package: AllelicImbalance) : scanForHeterozygotes

Identifies the positions of SNPs found in BamGR reads.

● Data Source: BioConductor
● Keywords: SNP, heterozygote, scan
● Alias: ASEset-scanForHeterozygotes, scanForHeterozygotes, scanForHeterozygotes,ASEset-method, scanForHeterozygotes,GAlignmentsList-method
● 0 images

ASEset.old (Package: AllelicImbalance) : ASEset.old object

old version of an ASEset which needs to be updated

● Data Source: BioConductor
● Keywords: data, example, object
● Alias: ASEset.old
● 0 images

ASEset.sim (Package: AllelicImbalance) : ASEset.sim object

ASEset with simulated data with SNPs within the first 200bp of chromosome 17, which is required to have example data for the refAllele function.

● Data Source: BioConductor
● Keywords: data, example, object
● Alias: ASEset.sim
● 0 images

ASEsetFromBam (Package: AllelicImbalance) : ASEset from bam file

count alleles and create an ASEset direct from bam file instead of reading into R first.

● Data Source: BioConductor
● Keywords: ASEset
● Alias: ASEsetFromBam, ASEsetFromBam,GRanges-method
● 0 images