Man pages for hyochoi/SCISSOR
Shape changes in selecting sample outliers in RNA-seq
| adj.center | Provide a center value adjusted by a lower bound |
| ADstat.hy | Provide the Anderson-Darling test statistic of standard... |
| ADstatWins.hy | Provide the winsorized Anderson-Darling test statistic |
| build_gaf | Build gene annotation |
| build_pileup | Build coverage pileup based on annotations |
| center_data | Centering data |
| detect_localout | Detect local shape outliers with a residual matrix |
| find.exon.hy | Finding exons and introns |
| generdir | written by – |
| get_offstat | Quantifying abnormal deletions in narrow regions |
| get_Ranges | Genomic ranges and locus ranges |
| getShiftParam | Shift parameter |
| get_sparsePD4one | Determining the most outlying structure using sparse basis... |
| get_SRcount | Count splice junction reads from BAM files |
| kdeplot.hy | kernel density function |
| len.intron.hy | Find intron length to be inserted |
| logtransform_data | Transforming data |
| miscGlobal | Detect global shape variants in RNA-seq inputData |
| miscLocal | Detect local shape changes |
| normalize_data | Normalizing log data |
| palette_SCISSOR | Palette for SCISSOR plots |
| PCnum.gamma.hy | Estimate the number principal components for RNA-seq |
| pd.rate.hy | Projection depth |
| plot_pileup | Plot pileup profiles |
| plot_ScissorOS | Plot outlyingness scores with a kernel density estimate |
| plot_ScissorSC | Plot shape changes from SCISSOR |
| process_pileup | Processing data |
| read_BAM | Read BAM files into R |
| RNAcurve | Plot RNA-seq curves |
| scale.factor | Obtain robust mean scale factors |
| Scissor | This function is a wrapper of the necessary functions to... |
