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 |