# Collection of Tools for Genomic Data Analysis

## Documentation for package ‘GenomicTools’ version 0.2.9.7

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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