Collection of Tools for Genomic Data Analysis


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Documentation for package ‘GenomicTools’ version 0.2.9.7

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R/GenomicTools-package Loose Collection of Expression and Genotype Analysis Tools, including (e)QTL and MDR.
annotTrack Example Annotation Track
eQTL Perform an eQTL Analysis
geneEXP Simulated Expression Data
genotData Simulated Genotype Data
getKEGGOrganisms Get a list of organisms in the KEGG database
getKEGGPathway Get a list of genes in a specific KEGG pathway.
getKEGGPathwayImage Get a visualization of a specific KEGG pathway.
getKEGGPathwayOverview Get a list of pathways in a specific organism.
getRSLocation Get the location of an SNP.
gtfToBed Extract the Chromosomal Information Required in bed Format from an imported gtf table.
mdr Perform a MDR.
mdrEnsemble Ensemble Classification Using an Existing MDR Object
mdrExample Example Data for MDR
phenoData Simulated Phenotype Data
plot-method Plot an eqtl Object
plot-method Plot an MDR Object
plot-method Plot an qtlRes Object
plot.eqtl Plot an eqtl Object
plot.mdr Plot an MDR Object
plot.qtlRes Plot an qtlRes Object
print-method Print an eqtl Object
print-method Print an mdr Object
print.eqtl Print an eqtl Object
print.mdr Print an mdr Object
QTL Perform a QTL Analysis
recodeData Recode a Genotype Data Matrix.
seqlength Get the sequence length of a fa-object.
summary-method Summarize an eqtl Object
summary.eqtl Summarize an eqtl Object