R Graphical Manual

Last data update: 2014.03.03

Data Source

R Release (3.2.3)
CranContrib
BioConductor
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Data Type

Packages
Functions
Images
Data set

Classification

Results 1 - 10 of 83 found.
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removeSequences (Package: strataG) : Remove Sequences

Remove sequences not used by samples listed in @loci slot.

● Data Source: CranContrib
● Keywords:
● Alias: removeSequences
● 0 images

fastsimcoal.input (Package: strataG) : Input functions for fastsimcoal parameters

Functions to create pop.info, locus.params, and hist.ev input matrices for fastsimcoal function.

● Data Source: CranContrib
● Keywords:
● Alias: fastsimcoal.input, fscHistEv, fscLocusParams, fscPopInfo
● 0 images

jackHWE (Package: strataG) : Hardy-Weinberg Equlibrium Jackknife

Test influence of samples on Hardy-Weinberg equilibrium via jackknife.

● Data Source: CranContrib
● Keywords:
● Alias: jackHWE, jackInfluential, plot.jack.influential
● 0 images

strataG-package (Package: strataG) : Summaries and population structure analyses of DNA sequence genotypic

strataG

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

privateAlleles (Package: strataG) : Private Alleles

The number of private alleles in each strata and locus.

● Data Source: CranContrib
● Keywords:
● Alias: privateAlleles
● 0 images

validIupacCodes (Package: strataG) : Valid IUPAC Codes

Get all possible valid IUPAC ambiguity codes for a set of nucleotide bases and ambiguity codes.

● Data Source: CranContrib
● Keywords:
● Alias: validIupacCodes
● 0 images

is.gtypes (Package: strataG) : Test if object is code{gtypes

Test if object is gtypes

● Data Source: CranContrib
● Keywords:
● Alias: is.gtypes
● 0 images

write.arlequin (Package: strataG) : Write Arlequin Input Files

Create an Arlequin-formatted input file from a gtypes object.

● Data Source: CranContrib
● Keywords: internal
● Alias: .writeArlequinHeader, .writeArlequinMsats, .writeArlequinSequences, .writeArlequinStructure, arlequin, write.arlequin
● 0 images

qaqc (Package: strataG) : Quality Assurance/Quality Control

Conducts a suite of QA/QC tests. Summarizes missing data and homozygosity by individual and locus, and looks for duplicate genotypes (see dupGenotypes). For sequence data, identifies low frequency substitutions (see lowFreqSubs), and computes haplotype likelihoods (see haplotypeLikelihoods).

● Data Source: CranContrib
● Keywords:
● Alias: qaqc
● 0 images

lowFreqSubs (Package: strataG) : Low Frequency Substitutions

Check nucleotide sites for low frequency substitutions.

● Data Source: CranContrib
● Keywords:
● Alias: lowFreqSubs
● 0 images