SVcalling_wrapperFunc: Main function for the 'MaRyam' package.

In friendsofstrandseq/MaRyam: Genotyping Structural Variants from single-cell Strand-seq data.

Description

Wrapper function to run SV calling after having the NB parmeters and segment read counts.

Usage

SVcalling_wrapperFunc(bin.size, K, maximumCN, segmentsCounts, r, p, cellTypes,
  outputDir, haplotypeMode)

Arguments

bin.size	the size of the bins
K	The number of chromosomes (autosomes). #TODO I suggest that user can define what chromosome wants to analyze. So this parameter should take vector of chromosome IDs => c(1:22,'X') or paste0('chr', c(1:22,'X'))
maximumCN	Maximum CN in the segments for SV calling. #TODO make sure parameters correspond to maxCN paramter in getCNprob
segmentsCounts	The dataframe containing the segments chr and coordinates and W and C read counts over all cells
r	The matrix of dispersion parameters of chromosomes(rows) and cells(columns) for CN=2 for a segment of size bin.size
p	The p parameter of the NB distribution
cellTypes	The matrix of cell types of chromosomes(rows) and cells(columns) TODO ... In function getSegType there is a parameter cellType. Are these paramters expecting the same thing? If not please use bit more informative name.
outputDir	The outputDir containing the input and output files.
haplotypeMode	a binary parameter showing wether we have the haplotype of WC cell types TODO ... #There is a haplotypeMode parameter in newSVcalling function. I guess they point to the same parameter.

Author(s)

Maryam Ghareghani

friendsofstrandseq/MaRyam documentation built on May 28, 2019, 8:40 p.m.