Genomic Random Interval (GRIN)

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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