Man pages for ShixiangWang/sigminer
Capture Genomic Variation Signatures using Non-Negative Matrix Factorization

centromeres.hg19location of centromeres at genome build hg19
centromeres.hg38location of centromeres at genome build hg38
chromsize.hg19chromosome size of genome build hg19
chromsize.hg38chromosome size of genome build hg38
CopyNumber-classClass CopyNumber
draw_cn_componentsPlot mixture fit model components
draw_cn_distributionPlot copy number distribution either by length or chromosome
draw_cn_featuresPlot copy number feature distribution
draw_features_corrplotDraw corrplot for signature activity and other features
draw_sig_activityPlot signature activity
draw_sig_corrplotPlot correlation between signature activities
draw_sig_enrichmentPlot signature enrichment result
draw_sig_profilePlot signature profile
draw_subtypes_comparisonPlot comparison between signature subtypes
filter_enrichmentFilter enrichment result
GenomicVariation-classClass GenomicVariation
get_adj_pGet adjust p values from group comparison
get_ArmLocationGet chromosome arm location
get_cnlistExtract copy number profile as list from CopyNumber object
get_cnsummary_sampleGet summary of copy number variation per sample
get_componentsFit optimal number of mixture model components
get_featuresDerive copy number feature distributions
get_LengthFractionCalculate length fraction profile of copy number
get_matrixGenerate a sample-by-component matrix
helloSay hello to users
MAF-classClass MAF
pipePipe operator
prepare_copynumberPrepare nmf input matrix for copy number signature analysis
prepare_mafPrepare nmf input matrix for mutational signature analysis
read_copynumberRead absolute copy number profile
read_mafRead MAF files.
read_variationRead genomic variation profile
sig_assign_samplesReturn sample clustering from NMF run results
sig_estimateEstimate signature number
sig_extractExtract variation signatures
sig_get_activityGet signature activity
sig_get_correlationGet correlation matrix between signature activities
sig_get_similarityGet similarity between signatures
sig_group_enrichmentPerforms alteration enrichment analysis for a given group
sigminersigminer: Capture Genomic Variation Signatures using...
sig_preparePrepare variation signature analysis
sig_summarize_correlationCalculate association between signature activity and other...
sig_summarize_subtypesGet summary of signature subtypes
sig_tidy_correlationTidy signature correlation results
subset.CopyNumberSubsetting CopyNumber object
test_run_componentsTest running status for getting components
ShixiangWang/sigminer documentation built on July 12, 2019, 12:08 p.m.