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| all.qn | Normalized exon level data |
| amp.spec.qn | Quantile normalization function on amplicons |
| ampmap | Mapping between amplicons and exons |
| badamp | Matrix for finding out the bad amplicons |
| calc.pp.bp | Function for calculating posterior probablilities for a list of base positions |
| calc.pp.bp.2 | Function for second round calculation of posterior probablilities for a list of base positions. |
| call.genotype | Wrapper function of performing multi-array analysis |
| call.ref.base | Function for a naive base caller used to calculate reference call rate |
| celint.qn | quantile normalized intensities for each base |
| correct.lr | Function for performing the adjustment of logratios using linear regression |
| correct.lr.singlebp | Function for correcting logratios for single chip with determined principal alternative alelles. |
| cross.chip | Function for cross-chip genotype calling. |
| dbsnp.info | Example dbSNP dataset used in SRMA pipeline of analyzing array-based sequencing array |
| explore.qc | Function for plotting qc measures for individual sample |
| find.badamps | Function for finding bad amplicons |
| find.best.fit | Function to select the best model fit |
| find.indels | Function to find insertion/deletions. |
| get.delta.sigma | Function for getting delta and sigma for each base |
| get.delta.sigma.qn | Wrapper function for getting quantitle normalized delta and sigma for each base |
| get.intensity | Function for getting raw or quantile normalizated intensities for each base |
| get.qc.measures.amplevel | Function for calculatig amplicon specific QC measures |
| get.qc.measures.baselevel | Function for preparing the measures used for quality assessment of DNA targets and resequencing arrays |
| get.qm | Function for calculating quality measures for an amplicon |
| initialize-method | Class "SRMAResults" |
| normalized.base.measures | A high-level function for getting delta and sigma for each base |
| post.process | Wrapper function for output analysis |
| quality.control | A high-level function for identifying bad amplicons using raw intensities from CEL files |
| ref.info | Example dataset containing reference allele information that are used in SRMA pipeline of analyzing array-based sequencing array |
| reorg.dat | Normalized dataset for downstream analysis |
| reorganize.datafiles | Function for reorganizing normalized data into array formats |
| sd.adj.dat | Normalized dataset |
| show-method | Class "SRMAResults" |
| single.array.lm.all.alleles | A function for adjusting for logratios for all bases on a single array |
| single.chip.posterior.prob | Wrapper function for adjustment of logratios for all bases using linear model |
| srma | Function for Sequencing Robust Multi-array Analysis. |
| SRMAResults-class | Class "SRMAResults" |
| summary-method | Class "SRMAResults" |
| write.srma | Function to write final SNV calls and Indel calls to tables |