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SNP

Parent category Analysis
Description SNP analysis
Component Version Inputs Outputs Description
AffySNPFetch 1.0 markernames, connection rsnumbers Fetches SNP rs-numbers from Ensembl based on Affy SNP-ids.
AlleleCounter 1.2.1 genotypes frequencies, naDist Calculates genotype frequencies of a SNPMatrix.
GenotypeComparator 1.7 caseF, controlF statistics Compares the allele and genotype differences between two sets of genotype frequencies.
MarkerCorrelations 1.1 genotypes markerGroups, keyMarkers Combines correlating markers from the SNPMatrices.
NextGene 1.5.1 sourceKeys, connection bioAnnotation Finds the closest gene, exon, or transcript for the given loci.
Plink 1.1 pedFile, mapFile, file1, file2, file3 result1, result2, result3, result4, result5 Wraps Plink software that allows various genome wide SNP data manipulations and analyzes.
RefSNPAnnotator 1.1.3 rsIDs annotations, geneChanges, databases Fetches annotations for given SNP rsID's with biomaRt.
SNPArrayReader 1.7 dataDir, sampleNames genotypeMatrix, markerNames, copynumberMatrix, probeAnnotation Imports genotype data from Illumina SNP and Affymetrix SNP 6.0 or 5.0 files.
SNPHelistinReader 1.2 sampleNames, markerNames, config genotypes Imports genotype data from a SNPHelistin database.
SNPKaplanMeier 1.6.1 genotypes, survival, annotations statistics, report Calculates Kaplan-Meier estimates for genotype specific survival effects.

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