Genomic Random Interval (GRIN)


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Documentation for package ‘GRIN2’ version 2.0.0

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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
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 Get Ensembl Gene and Regulatory Features Annotation Data
grin.assoc.lsn.outcome Associate Lesions with Clinical Outcomes
grin.barplt GRIN Lesion Stacked Bar Plot
grin.lsn.boundaries GRIN Evaluation of Lesion Boundaries
grin.oncoprint.mtx GRIN OncoPrint-Compatible Lesion Matrix
grin.stats Execute GRIN Statistical Framework
grin.stats.lsn.plot GRIN Statistics Lesions Plot
hg38_chrom_size Chromosome Length Data (hg38)
hg38_cytoband GRCh38 Chromosome Cytobands
hg38_gene_annotation Example Gene Annotation Data File
KW.hit.express Associate Lesion Groups with Gene Expression
lesion_data Example T-ALL Lesion Dataset
lsn.transcripts.plot Plot of Gene Lesions and Transcripts
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 Top Significant Genes
write.grin.xlsx Write GRIN Results to Excel File