Man pages for daewoooo/SaaRclust
R Package to cluster long sequencing reads into chromosomes to facilitate de novo genome assembly.
| clusters2ranges | Convert saarclust object into 'GRanges-class' object. |
| collapseBins | Collapse consecutive bins with the same ID value |
| countDirectionalReads | Count directional reads. |
| countProb | Calculate probability of PacBio reads having WW, CC or WC... |
| countProbOld | Calculate probability of PacBio reads having WW, CC or WC... |
| counts2ranges | Report W & C counts and cluster ID as 'GRanges-class' object. |
| EMclust | EM (Expectation maximization) function |
| estimateTheta | Estimate theta values based on hard clustering |
| exportClusteredReads | Print names of long reads into separate files based on soft... |
| exportGenomicLocations | Export best cluster IDs for each PB read |
| filterInput | Filter input data from the minimap |
| findAntiparallelClusters | Get pairs of clusters likely coming from the same chromosome... |
| findClusterPartners | Get pairs of clusters coming from the same chromosome that... |
| findClusterPartners2 | Get pairs of clusters coming from the same chromosome with... |
| findClusterPartners_maxMatch | Get pairs of clusters coming from the same chromosome that... |
| findClusterPartners_simple | Get pairs of clusters coming from the same chromosome with... |
| findSplitedClusters | Get pairs of clusters likely coming from the same chromosome |
| flipCounts | Reverse orientation of directional read counts |
| gammaFunction | Calculate gamma function of EM algorithm |
| getClusterAcc | Check clustering accuracy |
| getClusterIdentityPerChr | Export corresponding clusters for true chromosome |
| getClusterIdentityPerChrPerDir | Export corresponding cluster for true chromosome and... |
| getQualMeasure | Obtain summary measures of minimap output. |
| getRepresentativeAlignments | Import representative PacBio alignments. |
| hardClust | Hard clustering using k-means |
| hardClustAccuracy | Computes the performance of the hard clustering algorithm |
| importBams | Import BAM(s) and count reads |
| importData | Import pre-processed output from the minimap |
| importOldTestData | Import old output from the minimap |
| importTestData | Import output from the minimap |
| kahansum | Alternative sum function to reduce numerical error caused by... |
| maxWandCratiosFeatures | Get the feature vector based on the maxW,C ratios |
| mergeClusters | Hierarchical clustering for merging the kmeans clusters. |
| mergeSplitedClusters | Merge splitted clusters |
| plotClustAccuracy | Plot accuracy of clustring in respect to known location of... |
| plotHeatmap | Plot heatmap of responsibilities of each PB reads for each... |
| plotQualMeasure | Plot data quality measures. |
| plotReadAlignments | Plot coverage of short reads mapped on top of PB reads |
| plotReadMappingDist | Plot distribution of short reads mapped on top of PB reads |
| plotThetaEstimates | Plot theta estimates resulting from EM algorithm. |
| randomTheta | Simulate random theta estimates for cell type |
| readBamFileAsGRanges | Import BAM file into GRanges |
| rescaleTheta | Rescale theta values for WC cell type |
| runSaaRclust | Wrapper function to run saarclust pipeline. |
| SaaRclust | Wrapper function to run saarclust pipeline for a given number... |
| thetaRescale | Rescale theta values for WC cell type. |
| WandCratiosFeatures | Get the feature vector based on both W and C ratios |
| WminusCratiosFeatures | Get the feature vector based on the WmiunsC ratios |
