Man pages for friendsofstrandseq/MaRyam
Genotyping Structural Variants from single-cell Strand-seq data.
| addJumpProbs | Computes the probabilities of having the same... |
| allStatus | Generates all binary strings with n 0s and m 1s. |
| bam2ranges | Import BAM file into GRanges |
| changeCellTypesFormat | Changes the format of the cell types file and gives as output... |
| changeNBparamsFormat | Changes the format of the NB parameters and gives as output p... |
| changeRCformat | Changes the format of all files to the format used in the SV... |
| chrNumber | returns the number of a chromosome, given the input string |
| countAndNBfit_wrapperFunc | Counts the number of Watson and Crick reads of single cells... |
| decodeStatus | Converts a binary status to an integer vector status. |
| dispersionPar | Compute the dispersion paramters, given a segment type. |
| estimateP | Estimates p parameter and saves the empirical mean-var plot... |
| estimateR | Estimates r parameters |
| filt | Filters the list of data.frames based on the list od indexes. |
| genotype_class | returns the genotyoe class (CN_loss, CN_gain, normal_CN2, or... |
| getCNprob | Generate a CN probability vector. |
| getGenotypeProbDataFrame | Takes as input a haplotype probTable and outout the genotype... |
| getGenotypeProbTable | Compute a noramlInvCN probability table given the haplotype... |
| getGenotypeStatus | Computes the total normal CN and inverted CN status... |
| get_GT_class_prob_table | returns the genotyoe class (CN_loss, CN_gain, normal_CN2, or... |
| getlegend | helper function for heatmap |
| getNextState | Computes the next binary status of a given status with equal... |
| getPossibleCNs | Returns all CNs with maximum probability. |
| getSegReadCounts | outputs the segment counts |
| getSegType | Compute the segment type given a cell (majority) type and the... |
| initialState | Returns the first binary string with n 01 and m 1s. |
| jumpProbs | For each segment, computes the probabilities of having the... |
| newgetCellStatProbabilities | Returns a matrix of haplotype (rows) pobabilities in... |
| newgetGenotypeProbTable | Compute a genotype probability table given the haplotype... |
| newSVcalling | Takes as an input an aggregate prob table and call each... |
| nonzeroCovBins | Outputs the list of indices of the bins with non zero... |
| normalizeProbTable | Normalize a probability table to a table in which each column... |
| plotHeatmapSegment | Main heatmap function |
| readBams | Read bam files from a directory and output them (the first... |
| regularizeProbTable | We assume that the posteriori probability for different... |
| setPanelHeights | helper function for heatmap |
| sisterHaplotype | Takes as an input a haplotype state and returns the opposite... |
| SVcalling_wrapperFunc | Main function for the 'MaRyam' package. |
| uniqueMappableBins | Outputs the list of indices of the bins having the fraction... |
| WCreadCounts | Count the number of Watson and Crick reads and return a... |
