Man pages for KrasnitzLab/CNprep
Pre-process DNA Copy Number (CN) Data for Detection of CN Events
| annotexample | Annotation table for ROMA CGH platform and human genome... |
| applyCNPmask | Apply a mask to a table of copy number events. |
| breakIntoCNPs.chrom | Determine which segments have to be removed and redistribute... |
| breakIntoGaps | Redistribute probes/bins in removed segments into the... |
| centerprob | TODO |
| CNclusterNcenter | TODO |
| cnpexample | Example of a boundary positions table. |
| CNprep-package | CNprep: Pre-process DNA Copy Number (CN) Data for Detection... |
| CNpreprocessing | Pre-process DNA copy number (CN) data for detection of CN... |
| consolidate | Join clusters until the minimum degree of overlap is reached |
| containment.indicator | Idenfication oflower threshold segments to retain |
| EMexample | A model-based clustering |
| get.center | Group clusters together until the main cluster contain the... |
| getz | TODO |
| makeCNPmask | Given a set of copy-number events, create a DNA copy-number... |
| makeCNPmask.chrom | Given a set of copy-number events, create a DNA copy-number... |
| normalComparison | TODO |
| normsegs | A reference set of segments |
| ratexample | Example of copy number log ratio dataset |
| segexample | Example of a segmented copy number table |
| segsample | Calculate the median of the sampled copy number values from... |
| smad | Calculate the median absolute deviation of the values from a... |
| smedian | Calculate the median of the values from a contiguous... |
| smedian.sample | Calculate the median of the sampled values with replacement... |
| smedmad | Calculate the median and median absolute deviation of the... |
| validateCNpreprocessing | Parameters validation for the 'CNpreprocessing' function |
| validateMakeCNPmask | Parameters validation for the 'makeCNPmask' function |
| weighted.median | Calculate the lower weighted median of a specified vector. |
