# Genomic Random Interval (GRIN)

## Documentation for package ‘GRIN2’ version 2.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS

## Help Pages

alex.boxplots | Generate Box Plots of Gene Expression by Lesion Groups
alex.pathway | Visualize Lesion and Expression Data by Pathway
alex.prep.lsn.expr | Prepare Lesion and Expression Data for Kruskal-Wallis Test
alex.waterfall.plot | Generate Waterfall Plot of Lesion and Expression Data
alex.waterfall.prep | Prepare Lesion and Expression Data for Waterfall Plots
clin_data | Example Clinical Dataset for T-cell Acute Lymphoblastic Leukemia (T-ALL)
compute.gw.coordinates | Compute Genome-wide Plotting Coordinates
count.hits | Count Gene-Lesion Hits
default.grin.colors | Assign Default GRIN Colors
example_exon_annotation | Example Human Exon Annotation Data
expr_data | Example T-ALL Gene Expression Dataset
find.gene.lsn.overlaps | Find Gene-Lesion Overlaps
genomewide.log10q.plot | Genome-wide -log10(q-value) Plot
genomewide.lsn.plot | Genome-wide Lesion Plot
get.chrom.length | Get Chromosome Length
get.ensembl.annotation | Retrieve Ensembl Annotation Data
grin.assoc.expr.outcome | Association Between Gene Expression and Clinical Outcomes
grin.assoc.lsn.outcome | Associate Binary Genomic Lesions with Clinical Outcomes
grin.barplt | GRIN Lesion Stacked Bar Plot
grin.logRank | Log-Rank Test for Associations Between Genomic Lesions and Survival Outcomes
grin.lsn.boundaries | GRIN Evaluation of Lesion Boundaries
grin.oncoprint.mtx | GRIN OncoPrint-Compatible Lesion Matrix
grin.results | Example GRIN2 Analysis Results
grin.stats | Execute the GRIN Statistical Framework
grin.stats.lsn.plot | GRIN Lesion and Statistics Plot
hg38_chrom_size | Chromosome Length Data (GRCh38)
hg38_cytoband | GRCh38 Chromosome Cytobands
hg38_exon_chrom_size | Human GRCh38 Chromosome-Level Exon Target Sizes
hg38_gene_annotation | Example Gene Annotation Data
KW.hit.express | Associate Lesion Groups with Gene Expression
lesion_data | Example T-ALL Lesion Dataset
lsn.transcripts.plot | Plot Genomic Lesions with Transcript Annotations
onco.print.props | Oncoprint Proportions by Lesion Type
order.index.gene.data | Order and Index Gene Annotation Data
order.index.lsn.data | Order and Index Lesion Data
pathways | Genes Annotated to Biological Pathways
prep.binary.lsn.mtx | Prepare Binary Lesion Matrix
prep.gene.lsn.data | Prepare Gene and Lesion Data for GRIN Analysis
prep.lsn.type.matrix | Prepare Lesion Type Matrix
prob.hits | Find Probability of Locus Hit
top.alex.waterfall.plots | Generate Waterfall Plots for Significant Genes
write.grin.xlsx | Write GRIN Results to an Excel File