| 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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SNP