Man pages for friendsofstrandseq/MaRyam
Genotyping Structural Variants from single-cell Strand-seq data.

addJumpProbsComputes the probabilities of having the same...
allStatusGenerates all binary strings with n 0s and m 1s.
bam2rangesImport BAM file into GRanges
changeCellTypesFormatChanges the format of the cell types file and gives as output...
changeNBparamsFormatChanges the format of the NB parameters and gives as output p...
changeRCformatChanges the format of all files to the format used in the SV...
chrNumberreturns the number of a chromosome, given the input string
countAndNBfit_wrapperFuncCounts the number of Watson and Crick reads of single cells...
decodeStatusConverts a binary status to an integer vector status.
dispersionParCompute the dispersion paramters, given a segment type.
estimatePEstimates p parameter and saves the empirical mean-var plot...
estimateREstimates r parameters
filtFilters the list of data.frames based on the list od indexes.
genotype_classreturns the genotyoe class (CN_loss, CN_gain, normal_CN2, or...
getCNprobGenerate a CN probability vector.
getGenotypeProbDataFrameTakes as input a haplotype probTable and outout the genotype...
getGenotypeProbTableCompute a noramlInvCN probability table given the haplotype...
getGenotypeStatusComputes the total normal CN and inverted CN status...
get_GT_class_prob_tablereturns the genotyoe class (CN_loss, CN_gain, normal_CN2, or...
getlegendhelper function for heatmap
getNextStateComputes the next binary status of a given status with equal...
getPossibleCNsReturns all CNs with maximum probability.
getSegReadCountsoutputs the segment counts
getSegTypeCompute the segment type given a cell (majority) type and the...
initialStateReturns the first binary string with n 01 and m 1s.
jumpProbsFor each segment, computes the probabilities of having the...
newgetCellStatProbabilitiesReturns a matrix of haplotype (rows) pobabilities in...
newgetGenotypeProbTableCompute a genotype probability table given the haplotype...
newSVcallingTakes as an input an aggregate prob table and call each...
nonzeroCovBinsOutputs the list of indices of the bins with non zero...
normalizeProbTableNormalize a probability table to a table in which each column...
plotHeatmapSegmentMain heatmap function
readBamsRead bam files from a directory and output them (the first...
regularizeProbTableWe assume that the posteriori probability for different...
setPanelHeightshelper function for heatmap
sisterHaplotypeTakes as an input a haplotype state and returns the opposite...
SVcalling_wrapperFuncMain function for the 'MaRyam' package.
uniqueMappableBinsOutputs the list of indices of the bins having the fraction...
WCreadCountsCount the number of Watson and Crick reads and return a...
friendsofstrandseq/MaRyam documentation built on May 9, 2018, 8:34 p.m.