Capture Genomic Variation Signatures using Non-Negative Matrix Factorization

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Documentation for package ‘sigminer’ version 0.1.11

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sigminer-package sigminer: Capture Genomic Variation Signatures using Non-Negative Matrix Factorization
centromeres.hg19 location of centromeres at genome build hg19
centromeres.hg38 location of centromeres at genome build hg38
chromsize.hg19 chromosome size of genome build hg19
chromsize.hg38 chromosome size of genome build hg38
CopyNumber Class CopyNumber
CopyNumber-class Class CopyNumber
draw_cn_components Plot mixture fit model components
draw_cn_distribution Plot copy number distribution either by length or chromosome
draw_cn_features Plot copy number feature distribution
draw_sig_activity Plot signature activity
draw_sig_corrplot Plot correlation between signature activities
draw_sig_profile Plot signature profile
draw_subtypes_comparison Plot comparison between signature subtypes
GenomicVariation Class GenomicVariation
GenomicVariation-class Class GenomicVariation
get_ArmLocation Get chromosome arm location
get_cnlist Extract copy number profile as list from CopyNumber object
get_cnsummary_sample Get summary of copy number variation per sample
get_components Fit optimal number of mixture model components
get_features Derive copy number feature distributions
get_LengthFraction Calculate length fraction profile of copy number
get_matrix Generate a sample-by-component matrix
hello Say hello to users
MAF Class MAF
MAF-class Class MAF
prepare_copynumber Prepare nmf input matrix for copy number signature analysis
prepare_maf Prepare nmf input matrix for mutational signature analysis
read_copynumber Read absolute copy number profile
read_maf Read MAF files.
read_variation Read genomic variation profile
sigminer sigminer: Capture Genomic Variation Signatures using Non-Negative Matrix Factorization
sig_assign_samples Return sample clustering from NMF run results
sig_estimate Estimate signature number
sig_extract Extract variation signatures
sig_get_activity Get signature activity
sig_get_correlation Get correlation matrix between signature activities
sig_get_similarity Get similarity between signatures
sig_prepare Prepare variation signature analysis
sig_prepare.CopyNumber Prepare variation signature analysis
sig_prepare.GenomicVariation Prepare variation signature analysis
sig_prepare.MAF Prepare variation signature analysis
sig_summarize_subtypes Get summary of signature subtypes
subset.CopyNumber Subsetting CopyNumber object
test_run_components Test running status for getting components