# Genomic Random Interval (GRIN)

## Documentation for package ‘GRIN2’ version 1.0

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

## Help Pages

alex.boxplots | Prepare Box Plots of Expression Data by Lesion Groups
alex.pathway | Associate Lesions with Expression Data on the Pathway Level
alex.prep.lsn.expr | Prepare Lesion and Expression Data for Kruskal-Wallis Test
alex.waterfall.plot | Prepare Waterfall Plot of Lesion and Expression Data
alex.waterfall.prep | Prepare Lesion and Expression Data for Waterfall Plots
clin.data | Example T-ALL Dataset Clinical Data
compute.gw.coordinates | Compute Genome-wide Coordinates
count.hits | Count Gene Lesion Hits
default.grin.colors | Default GRIN Colors
expr.data | Example T-ALL Dataset Gene Expression Data
find.gene.lsn.overlaps | Find Gene Lesion Overlaps
genomewide.log10q.plot | Genomewide log10q Plot
genomewide.lsn.plot | Genome-wide Lesion Plot
get.chrom.length | Get Chromosome Length
get.ensembl.annotation | Get Ensembl Gene and Regulatory Features Annotation Data
grin.assoc.lsn.outcome | Associate Lesions with Clinical Outcomes
grin.barplt | GRIN Bar Plot
grin.lsn.boundaries | GRIN Evaluate Lesion Boundaries
grin.oncoprint.mtx | GRIN OncoPrint Matrix
grin.stats | GRIN Statistics Output
grin.stats.lsn.plot | GRIN Statistics Lesions Plot
hg19.chrom.size | Chromosome Length Data File
hg19.gene.annotation | Example Gene Annotation Data File
hg19_cytoband | GRCh37 Chromosome Cytobands
hg38_cytoband | GRCh38 Chromosome Cytobands
KW.hit.express | Associate Lesion with Expression Data Using Kruskal-Wallis Test
lesion.data | Example T-ALL Dataset Lesion Data
lsn.transcripts.plot | Lesions Gene Transcripts Plot
onco.print.props | Oncoprint proportions
order.index.gene.data | Order Index Gene Data
order.index.lsn.data | Order Index Lesion Data
pathways | List of Genes Annotated to a Group of Pathways
prep.binary.lsn.mtx | Prepare Binary Lesion Matrix
prep.gene.lsn.data | Prepare Gene and Lesion Data
prep.lsn.type.matrix | Prepare Lesion Type Matrix
prob.hits | Find Probablity of Locus Hit
top.alex.waterfall.plots | Waterfall Plots for Lesion and Expression Data of Top Significant Genes
write.grin.xlsx | Write GRIN Results